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Gadolinium in PDB 4ahx: FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface

Protein crystallography data

The structure of FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface, PDB code: 4ahx 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) 18.55 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.230, 62.150, 105.800, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.3

Other elements in 4ahx:

The structure of FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Gadolinium Binding Sites:

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

Gadolinium binding site 1 out of 9 in 4ahx

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Gadolinium binding site 1 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1272

b:10.5
occ:0.80
 OD1 A:ASP160 2.3 11.1 0.5
O A:TRP228 2.3 8.4 1.0
OD1 A:ASP160 2.3 15.2 0.5
OD1 A:ASP161 2.3 9.5 1.0
OD1 A:ASN224 2.4 9.1 1.0
O A:HOH2343 2.4 10.4 0.5
O A:VAL226 2.4 9.1 1.0
O A:HOH2282 2.5 17.2 0.5
O A:HOH2284 2.5 12.3 1.0
O A:HOH2281 2.5 13.2 1.0
CG A:ASP161 3.3 9.1 1.0
CG A:ASP160 3.4 15.2 0.5
CG A:ASP160 3.4 12.7 0.5
CG A:ASN224 3.4 8.1 1.0
C A:TRP228 3.5 8.2 1.0
C A:VAL226 3.6 8.9 1.0
OD2 A:ASP161 3.7 10.4 1.0
OD2 A:ASP160 3.8 18.3 0.5
ND2 A:ASN224 3.9 8.4 1.0
OD2 A:ASP160 3.9 15.8 0.5
N A:TRP228 4.2 8.5 1.0
O A:HOH2195 4.2 17.6 0.5
N A:VAL226 4.2 9.0 1.0
CA A:TRP228 4.4 9.2 1.0
C A:SER227 4.4 9.0 1.0
CA A:VAL226 4.4 10.3 1.0
OG A:SER227 4.5 9.6 1.0
O A:HOH2132 4.5 14.3 0.5
O A:HOH2136 4.5 16.5 0.8
N A:GLY229 4.5 9.4 1.0
O A:HOH2285 4.6 26.0 1.0
C A:ASP160 4.6 10.4 1.0
CB A:ASP160 4.7 12.1 0.5
O A:SER227 4.7 8.2 1.0
CA A:GLY229 4.7 9.9 1.0
N A:SER227 4.7 8.3 1.0
CB A:ASP161 4.7 9.6 1.0
CB A:ASP160 4.7 13.5 0.5
O A:ASP160 4.8 10.1 1.0
N A:ASP161 4.8 9.9 1.0
CB A:ASN224 4.8 8.2 1.0
CB A:TRP228 4.9 9.4 1.0
CB A:VAL226 4.9 11.2 1.0
N A:ALA225 4.9 9.4 1.0
CA A:ASP160 5.0 11.2 0.5
CA A:ASP160 5.0 11.7 0.5

Gadolinium binding site 2 out of 9 in 4ahx

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Gadolinium binding site 2 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1273

b:12.6
occ:0.50
 OD1 A:ASP78 2.3 24.8 0.9
OD2 A:ASP245 2.3 18.2 0.9
OD1 A:ASP245 2.4 17.5 0.9
O A:HOH2167 2.5 24.6 1.0
O A:HOH2155 2.5 25.2 1.0
O A:HOH2153 2.5 15.5 1.0
O A:HOH2156 2.5 26.6 1.0
O A:HOH2360 2.5 26.5 1.0
O A:HOH2164 2.5 25.1 1.0
CG A:ASP245 2.8 18.0 0.9
CG A:ASP78 3.4 25.9 0.9
OD2 A:ASP78 4.0 29.6 0.9
O A:HOH2398 4.3 30.1 1.0
CB A:ASP245 4.3 15.4 0.9
O A:SER80 4.5 12.9 1.0
CB A:ASP78 4.5 20.1 0.9
O A:HOH2166 4.6 41.6 1.0
OD2 A:ASP82 4.6 11.9 0.5
O A:HOH2168 4.6 43.2 1.0
C A:ASP78 4.8 15.3 1.0
O A:ASP78 4.9 16.1 1.0
CB A:SER80 4.9 11.1 1.0
N A:SER80 4.9 10.8 1.0

Gadolinium binding site 3 out of 9 in 4ahx

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Gadolinium binding site 3 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1274

b:13.3
occ:0.50
 O A:HOH2162 2.3 11.4 0.5
OD2 A:ASP125 2.3 19.6 1.0
O A:ACT1282 2.3 15.8 0.7
OD1 A:ASP82 2.3 9.4 0.5
OXT A:ACT1282 2.4 12.6 0.7
O A:ASP82 2.4 14.2 1.0
OD1 A:ASP125 2.4 21.1 1.0
O A:HOH2163 2.5 15.5 0.5
O A:HOH2165 2.6 13.7 0.5
C A:ACT1282 2.7 14.2 0.7
CG A:ASP125 2.7 15.9 1.0
CG A:ASP82 3.4 11.6 0.5
C A:ASP82 3.5 12.9 1.0
O A:HOH2247 3.6 16.5 0.5
CB A:ASP82 3.9 11.9 0.5
GD A:GD1275 3.9 11.3 0.4
O A:HOH2164 4.0 25.1 1.0
CA A:ASP82 4.1 11.8 0.5
O A:HOH2248 4.2 28.0 1.0
N A:ASP82 4.2 12.5 1.0
CH3 A:ACT1282 4.2 13.2 0.7
CA A:ASP82 4.2 13.0 0.5
O A:HOH2166 4.3 41.6 1.0
CB A:ASP125 4.3 14.4 1.0
O A:HOH2176 4.3 12.8 1.0
CB A:ASP82 4.3 14.7 0.5
N A:TYR83 4.5 11.6 1.0
O A:ASP125 4.5 11.8 1.0
OD2 A:ASP82 4.5 11.9 0.5
CA A:TYR83 4.7 9.8 1.0
O A:HOH2178 4.8 30.8 1.0
O A:HOH2398 4.9 30.1 1.0

Gadolinium binding site 4 out of 9 in 4ahx

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Gadolinium binding site 4 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1275

b:11.3
occ:0.40
 O A:ACT1282 2.3 15.8 0.7
O A:ASP125 2.4 11.8 1.0
OD1 A:ASP125 2.4 21.1 1.0
O A:HOH2247 2.5 16.5 0.5
O A:HOH2399 2.5 35.5 1.0
O A:HOH2398 2.5 30.1 1.0
O A:HOH2249 2.5 33.0 1.0
O A:HOH2246 2.5 24.9 1.0
O A:HOH2242 2.6 21.9 1.0
C A:ASP125 3.3 11.3 1.0
C A:ACT1282 3.4 14.2 0.7
CG A:ASP125 3.4 15.9 1.0
CA A:ASP125 3.7 12.1 1.0
O A:HOH2165 3.7 13.7 0.5
GD A:GD1274 3.9 13.3 0.5
CH3 A:ACT1282 4.0 13.2 0.7
CB A:ASP125 4.1 14.4 1.0
O A:HOH2248 4.2 28.0 1.0
OXT A:ACT1282 4.3 12.6 0.7
OD2 A:ASP125 4.4 19.6 1.0
O A:HOH2251 4.5 37.4 1.0
N A:PHE127 4.5 12.5 1.0
O A:HOH2164 4.5 25.1 1.0
N A:LEU126 4.6 11.2 1.0
O A:HOH2154 4.6 32.8 1.0
O A:HOH2243 4.7 37.0 1.0
O A:THR124 4.8 12.2 1.0
O A:HOH2155 4.8 25.2 1.0

Gadolinium binding site 5 out of 9 in 4ahx

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Gadolinium binding site 5 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1276

b:60.4
occ:0.40
 OE2 A:GLU236 2.3 29.9 1.0
OE1 A:GLU236 2.4 35.7 1.0
O A:HOH2346 2.5 27.9 1.0
O A:HOH2347 2.5 40.4 1.0
O A:HOH2350 2.5 43.1 1.0
CD A:GLU236 2.7 26.6 1.0
CG A:GLU236 4.2 20.0 1.0
O A:HOH2349 4.5 32.3 1.0
O A:HOH2348 4.8 43.5 1.0

Gadolinium binding site 6 out of 9 in 4ahx

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Gadolinium binding site 6 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1277

b:21.5
occ:0.40
 O A:HOH2304 2.2 27.8 0.5
OE1 A:GLU179 2.3 23.3 1.0
OD1 A:ASP255 2.3 21.0 0.5
OE2 A:GLU179 2.3 21.8 1.0
O A:HOH2306 2.5 29.7 1.0
O A:HOH2302 2.5 50.7 1.0
O A:HOH2371 2.5 42.6 1.0
O A:HOH2303 2.6 30.4 0.5
CD A:GLU179 2.6 21.4 1.0
CG A:ASP255 3.3 19.9 0.5
OD1 A:ASP255 3.7 23.4 0.5
CG A:ASP255 3.9 21.3 0.5
OD2 A:ASP255 3.9 24.4 0.5
CG A:GLU179 4.2 18.3 1.0
CB A:ASP255 4.3 18.5 0.5
CB A:ASP255 4.4 17.6 0.5
OD2 A:ASP255 4.4 25.8 0.5
O A:HOH2373 4.4 26.0 1.0
CA A:ASP255 4.5 15.9 0.5
CA A:ASP255 4.5 15.4 0.5
O A:HOH2305 4.6 26.6 1.0
N A:ASP256 4.7 15.3 1.0
O A:HOH2374 4.8 34.6 1.0
CB A:GLU179 4.9 16.0 1.0

Gadolinium binding site 7 out of 9 in 4ahx

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Gadolinium binding site 7 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1278

b:15.2
occ:0.40
 O A:HOH2400 2.2 25.9 0.5
O A:HOH2287 2.2 11.1 0.5
OG A:SER170 2.3 16.7 1.0
OE2 A:GLU174 2.3 24.8 1.0
OE1 A:GLU174 2.4 25.0 1.0
O A:HOH2040 2.5 23.5 1.0
O A:HOH2292 2.5 45.2 1.0
O A:HOH2288 2.5 37.4 1.0
CD A:GLU174 2.7 18.3 1.0
CB A:SER170 3.5 15.2 1.0
CG A:GLU174 4.2 15.3 1.0
CA A:SER170 4.3 13.7 1.0
O A:HOH2291 4.3 31.3 1.0
OE2 A:GLU27 4.5 14.2 1.0
O A:HOH2042 4.5 16.7 1.0
O A:HOH2293 4.5 39.7 1.0
O A:HOH2294 4.8 39.7 1.0
O A:HOH2148 4.9 34.2 1.0
N A:SER170 4.9 14.0 1.0

Gadolinium binding site 8 out of 9 in 4ahx

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Gadolinium binding site 8 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1279

b:21.1
occ:0.20
 GD A:GD1279 0.0 21.1 0.2
GD A:GD1279 1.5 16.2 0.2
O A:HOH2171 2.5 20.1 1.0
O A:HOH2172 2.5 41.3 1.0
O A:HOH2401 2.5 71.8 1.0
O A:HOH2173 2.6 52.7 1.0
OD1 A:ASP82 2.6 15.9 0.5
O A:HOH2201 3.0 39.4 1.0
OD2 A:ASP82 3.5 19.4 0.5
CG A:ASP82 3.5 17.5 0.5
OE1 A:GLU99 3.6 17.6 1.0
O A:HOH2197 3.8 27.2 1.0
O A:HOH2170 4.2 18.0 1.0
OD1 A:ASN84 4.3 11.9 1.0
CD A:GLU99 4.5 16.6 1.0
OE2 A:GLU99 4.6 19.3 1.0
N A:GLN98 4.8 11.2 1.0
O A:HOH2174 4.8 24.2 1.0
ND2 A:ASN84 5.0 13.0 1.0

Gadolinium binding site 9 out of 9 in 4ahx

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Gadolinium binding site 9 out of 9 in the FLO5A Showing A Trinuclear Gadolinium Cluster on Its Surface


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 Trinuclear Gadolinium Cluster on Its Surface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1279

b:16.2
occ:0.20
 GD A:GD1279 0.0 16.2 0.2
GD A:GD1279 1.5 21.1 0.2
OD2 A:ASP82 2.3 19.4 0.5
OD1 A:ASP82 2.4 15.9 0.5
O A:HOH2173 2.5 52.7 1.0
O A:HOH2401 2.5 71.8 1.0
O A:HOH2172 2.5 41.3 1.0
O A:HOH2201 2.5 39.4 1.0
CG A:ASP82 2.8 17.5 0.5
O A:HOH2171 3.6 20.1 1.0
O A:HOH2174 4.3 24.2 1.0
CB A:ASP82 4.4 14.7 0.5
OE1 A:GLU99 4.6 17.6 1.0
OD1 A:ASN84 4.6 11.9 1.0
CB A:ASP82 4.7 11.9 0.5
O A:HOH2169 4.7 46.4 1.0
ND2 A:ASN84 4.7 13.0 1.0
O A:HOH2170 4.9 18.0 1.0
OE2 A:GLU99 4.9 19.3 1.0
O A:HOH2085 4.9 24.8 1.0

Reference:

M.Veelders, L.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 21:27:32 2024

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