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Gadolinium in PDB 4ai3: FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking

Protein crystallography data

The structure of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking, PDB code: 4ai3 was solved by M.Veelders, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.58 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.080, 64.190, 104.720, 90.00, 90.00, 90.00
R / Rfree (%) 16.618 / 22.23

Other elements in 4ai3:

The structure of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Gadolinium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Gadolinium atom in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking (pdb code 4ai3). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 11 binding sites of Gadolinium where determined in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking, PDB code: 4ai3:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gadolinium binding site 1 out of 11 in 4ai3

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Gadolinium binding site 1 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1272

b:8.2
occ:0.50
 O A:HOH2219 2.3 10.3 1.0
O A:TRP228 2.3 5.7 1.0
OD1 A:ASN224 2.3 3.8 1.0
OD1 A:ASP160 2.3 12.5 0.9
O A:VAL226 2.4 3.7 1.0
OD1 A:ASP161 2.4 6.2 1.0
O A:HOH2265 2.5 17.1 1.0
O A:HOH2217 2.5 6.9 1.0
CG A:ASP161 3.4 5.5 1.0
CG A:ASN224 3.4 3.0 1.0
CG A:ASP160 3.5 13.3 0.9
C A:TRP228 3.5 6.6 1.0
C A:VAL226 3.6 3.9 1.0
OD2 A:ASP161 3.7 6.0 1.0
ND2 A:ASN224 3.9 4.5 1.0
OD2 A:ASP160 3.9 20.1 0.9
N A:TRP228 4.2 5.6 1.0
N A:VAL226 4.2 4.2 1.0
O A:HOH2158 4.3 26.5 1.0
C A:SER227 4.3 4.6 1.0
CA A:TRP228 4.4 6.2 1.0
CA A:VAL226 4.4 4.8 1.0
OG A:SER227 4.5 2.0 1.0
O A:HOH2111 4.5 18.7 1.0
N A:GLY229 4.5 7.2 1.0
C A:ASP160 4.6 6.3 1.0
O A:SER227 4.6 3.2 1.0
O A:ASP160 4.7 5.7 1.0
N A:SER227 4.7 3.8 1.0
O A:HOH2220 4.7 25.7 1.0
CB A:ASP161 4.7 6.1 1.0
CB A:ASN224 4.7 2.9 1.0
N A:ASP161 4.7 5.0 1.0
CB A:ASP160 4.7 9.2 1.0
CA A:GLY229 4.8 6.1 1.0
N A:ALA225 4.8 3.0 1.0
CB A:VAL226 4.8 5.9 1.0
CB A:TRP228 4.9 6.5 1.0
CA A:ASP160 4.9 8.4 1.0
CA A:SER227 5.0 4.4 1.0

Gadolinium binding site 2 out of 11 in 4ai3

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Gadolinium binding site 2 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1273

b:17.6
occ:0.35
 O A:HOH2122 2.2 22.1 1.0
O A:HOH2123 2.2 26.7 1.0
OD1 A:ASP78 2.4 16.5 0.8
OD2 A:ASP245 2.4 15.2 0.7
O A:HOH2120 2.6 14.4 1.0
OD1 A:ASP245 2.6 11.3 0.7
O A:HOH2273 2.6 38.2 1.0
O A:HOH2126 2.6 36.6 1.0
CG A:ASP245 2.8 13.8 0.7
O A:HOH2139 2.8 31.1 1.0
CG A:ASP78 3.3 16.9 0.8
OD2 A:ASP78 3.5 22.4 0.8
GD A:GD1277 3.7 33.7 0.3
GD A:GD1278 3.9 22.3 0.3
GD A:GD1276 4.0 27.8 0.4
O A:HOH2305 4.2 25.8 1.0
CB A:ASP245 4.3 13.4 0.7
CB A:ASP245 4.4 13.2 0.3
O A:HOH2141 4.5 35.0 1.0
O A:SER80 4.6 8.6 1.0
CB A:ASP78 4.6 13.4 1.0
O A:HOH2121 4.8 26.4 1.0
O A:HOH2142 4.9 39.1 1.0
C A:ASP78 4.9 11.5 1.0
O A:ASP78 4.9 11.7 1.0
OD1 A:ASP82 5.0 15.1 0.7
CB A:SER80 5.0 7.0 1.0

Gadolinium binding site 3 out of 11 in 4ai3

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Gadolinium binding site 3 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1274

b:21.9
occ:0.40
 O A:HOH2132 2.2 24.3 1.0
OD1 A:ASP125 2.4 15.1 0.7
OD1 A:ASP82 2.4 15.1 0.7
O A:ASP82 2.4 6.2 0.3
O A:HOH2140 2.5 16.7 1.0
O A:HOH2192 2.5 24.7 1.0
O A:HOH2131 2.6 12.9 1.0
O A:ASP82 2.8 9.1 0.7
O A:HOH2139 3.1 31.1 1.0
CG A:ASP82 3.2 13.2 0.7
CG A:ASP125 3.3 15.0 0.7
GD A:GD1275 3.4 19.5 0.1
GD A:GD1279 3.5 25.4 0.3
OD2 A:ASP125 3.6 18.6 0.7
C A:ASP82 3.6 7.0 0.3
GD A:GD1276 3.6 27.8 0.4
C A:ASP82 3.7 8.6 0.7
OD2 A:ASP82 3.8 21.2 0.7
N A:ASP82 4.1 7.7 0.3
CB A:ASP82 4.1 7.4 0.3
N A:ASP82 4.1 8.4 0.7
O A:HOH2136 4.1 13.1 0.7
CA A:ASP82 4.2 7.3 0.3
CA A:ASP82 4.2 8.6 0.7
CB A:ASP82 4.2 9.4 0.7
O A:ASP125 4.3 11.7 1.0
O A:HOH2138 4.5 22.0 1.0
O A:HOH2127 4.5 21.2 1.0
CB A:ASP125 4.5 9.6 0.3
O A:HOH2142 4.6 39.1 1.0
OD2 A:ASP82 4.6 12.3 0.3
CB A:ASP125 4.7 10.5 0.7
O A:HOH2126 4.7 36.6 1.0
N A:TYR83 4.7 6.8 1.0
O A:HOH2306 4.8 23.2 1.0
O A:HOH2312 4.8 30.9 1.0
CG A:ASP82 4.9 8.9 0.3
CG A:ASP125 4.9 9.6 0.3
C A:ASP125 4.9 10.2 1.0
CA A:TYR83 5.0 5.7 1.0
O A:HOH2191 5.0 16.9 1.0

Gadolinium binding site 4 out of 11 in 4ai3

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Gadolinium binding site 4 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1275

b:19.5
occ:0.15
 O A:HOH2192 2.1 24.7 1.0
O A:ASP125 2.3 11.7 1.0
O A:HOH2304 2.5 14.4 0.5
O A:HOH2191 2.8 16.9 1.0
GD A:GD1276 3.2 27.8 0.4
OD1 A:ASP125 3.4 15.1 0.7
C A:ASP125 3.4 10.2 1.0
GD A:GD1274 3.4 21.9 0.4
CA A:ASP125 3.8 9.5 0.3
CA A:ASP125 3.9 10.3 0.7
CG A:ASP125 4.0 15.0 0.7
O A:HOH2140 4.1 16.7 1.0
O A:HOH2139 4.2 31.1 1.0
O A:HOH2131 4.3 12.9 1.0
O A:HOH2127 4.3 21.2 1.0
CB A:ASP125 4.4 9.6 0.3
GD A:GD1279 4.4 25.4 0.3
O A:HOH2122 4.5 22.1 1.0
N A:PHE127 4.5 9.3 1.0
O A:HOH2306 4.5 23.2 1.0
O A:HOH2190 4.5 29.2 1.0
O A:HOH2121 4.5 26.4 1.0
O A:HOH2310 4.5 33.4 1.0
CB A:ASP125 4.5 10.5 0.7
N A:LEU126 4.6 7.9 1.0
O A:HOH2308 4.6 15.7 0.5
OD1 A:ASP125 4.7 11.9 0.3
OD2 A:ASP125 4.7 18.6 0.7
O A:THR124 4.8 8.1 1.0
O A:HOH2132 4.9 24.3 1.0
CG A:ASP125 4.9 9.6 0.3
CA A:LEU126 5.0 7.7 1.0

Gadolinium binding site 5 out of 11 in 4ai3

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Gadolinium binding site 5 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1276

b:27.8
occ:0.40
 O A:HOH2305 2.3 25.8 1.0
O A:HOH2140 2.3 16.7 1.0
O A:HOH2139 2.4 31.1 1.0
O A:HOH2122 2.5 22.1 1.0
O A:HOH2192 2.6 24.7 1.0
O A:HOH2304 2.6 14.4 0.5
O A:HOH2306 2.6 23.2 1.0
GD A:GD1275 3.2 19.5 0.1
GD A:GD1274 3.6 21.9 0.4
O A:HOH2307 3.7 35.0 1.0
GD A:GD1279 3.7 25.4 0.3
O A:HOH2308 3.8 15.7 0.5
GD A:GD1277 3.8 33.7 0.3
GD A:GD1278 3.8 22.3 0.3
GD A:GD1273 4.0 17.6 0.3
O A:HOH2142 4.0 39.1 1.0
O A:HOH2123 4.2 26.7 1.0
OD1 A:ASP82 4.4 15.1 0.7
O A:HOH2120 4.5 14.4 1.0
O A:HOH2126 4.5 36.6 1.0
O A:HOH2191 4.5 16.9 1.0
O A:HOH2312 4.7 30.9 1.0
O A:HOH2310 4.7 33.4 1.0
O A:HOH2132 4.7 24.3 1.0
O A:HOH2309 4.8 29.9 1.0
OD2 A:ASP82 4.9 21.2 0.7
O A:HOH2121 4.9 26.4 1.0

Gadolinium binding site 6 out of 11 in 4ai3

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Gadolinium binding site 6 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1277

b:33.7
occ:0.35
 O A:HOH2123 2.5 26.7 1.0
O A:HOH2273 2.7 38.2 1.0
O A:HOH2305 2.7 25.8 1.0
O A:HOH2307 2.7 35.0 1.0
O A:HOH2142 3.2 39.1 1.0
GD A:GD1273 3.7 17.6 0.3
GD A:GD1276 3.8 27.8 0.4
O A:HOH2122 3.9 22.1 1.0
GD A:GD1278 3.9 22.3 0.3
O A:HOH2139 4.2 31.1 1.0
O A:HOH2306 4.3 23.2 1.0
O A:HOH2140 4.3 16.7 1.0
OD2 A:ASP245 4.5 15.2 0.7
O A:HOH2309 4.9 29.9 1.0
O A:HOH2126 4.9 36.6 1.0

Gadolinium binding site 7 out of 11 in 4ai3

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Gadolinium binding site 7 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1278

b:22.3
occ:0.30
 O A:HOH2308 2.3 15.7 0.5
O A:HOH2305 2.4 25.8 1.0
OD2 A:ASP78 2.4 22.4 0.8
O A:HOH2122 2.5 22.1 1.0
O A:HOH2309 2.6 29.9 1.0
O A:HOH2123 2.6 26.7 1.0
CG A:ASP78 3.4 16.9 0.8
O A:HOH2304 3.8 14.4 0.5
GD A:GD1276 3.8 27.8 0.4
GD A:GD1273 3.9 17.6 0.3
GD A:GD1277 3.9 33.7 0.3
OD1 A:ASP78 4.0 16.5 0.8
O A:HOH2121 4.6 26.4 1.0
CB A:ASP78 4.6 13.4 1.0
O A:HOH2124 4.6 34.9 1.0
O A:HOH2306 4.9 23.2 1.0
O A:HOH2139 5.0 31.1 1.0

Gadolinium binding site 8 out of 11 in 4ai3

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Gadolinium binding site 8 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1279

b:25.4
occ:0.35
 O A:HOH2192 2.3 24.7 1.0
O A:HOH2140 2.3 16.7 1.0
O A:HOH2312 2.5 30.9 1.0
O A:HOH2132 2.5 24.3 1.0
O A:HOH2306 2.6 23.2 1.0
O A:HOH2310 2.8 33.4 1.0
O A:HOH2311 2.8 26.6 1.0
GD A:GD1274 3.5 21.9 0.4
GD A:GD1276 3.7 27.8 0.4
O A:HOH2307 3.9 35.0 1.0
OD1 A:ASP125 3.9 15.1 0.7
O A:HOH2136 4.1 13.1 0.7
GD A:GD1275 4.4 19.5 0.1
O A:HOH2142 4.4 39.1 1.0
OD1 A:ASP125 4.5 11.9 0.3
O A:HOH2001 4.6 33.1 1.0
O A:HOH2146 4.7 7.5 0.5
O A:HOH2138 4.7 22.0 1.0
CG A:ASP125 4.9 9.6 0.3
O A:HOH2139 4.9 31.1 1.0
O A:HOH2305 5.0 25.8 1.0

Gadolinium binding site 9 out of 11 in 4ai3

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Gadolinium binding site 9 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 9 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1280

b:44.9
occ:0.30
 O A:HOH2266 2.3 34.3 1.0
OE2 A:GLU236 2.4 27.4 0.7
CD A:GLU236 3.3 20.0 0.7
OE1 A:GLU236 3.5 22.8 0.7
CG A:GLU236 4.6 14.2 1.0
CA A:GLY240 4.7 17.5 1.0
O A:GLY240 5.0 18.3 1.0

Gadolinium binding site 10 out of 11 in 4ai3

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Gadolinium binding site 10 out of 11 in the FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 10 of FLO5A Showing A Heptanuclear Gadolinium Cluster on Its Surface After 60 Min of Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1281

b:40.4
occ:0.30
 O A:HOH2233 2.2 31.3 1.0
O A:HOH2313 2.3 47.1 1.0
OE1 A:GLU179 2.4 24.7 1.0
O A:HOH2231 2.4 39.8 1.0
OE2 A:GLU179 2.6 20.5 1.0
CD A:GLU179 2.8 22.6 1.0
OD1 A:ASP255 3.9 16.5 0.5
CG A:ASP255 4.0 15.3 0.5
CB A:ASP255 4.1 14.4 1.0
CG A:GLU179 4.3 16.3 1.0
O A:HOH2283 4.5 29.3 1.0
CA A:ASP255 4.5 13.1 1.0
O A:HOH2232 4.6 22.3 1.0
OD2 A:ASP255 4.6 18.4 0.5
N A:ASP256 4.8 13.6 1.0
O A:HOH2284 4.9 38.6 1.0

Reference:

M.Veelders, L.-O.Essen. Complex Gadolinium-Oxo Clusters Formed Along Concave Protein Surfaces. Chembiochem V. 13 2187 2012.
ISSN: ISSN 1439-4227
PubMed: 22936626
DOI: 10.1002/CBIC.201200441
Page generated: Sat Aug 10 21:31:49 2024

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