Atomistry » Gadolinium » PDB 1b9x-4l12 » 4ahx
Atomistry »
  Gadolinium »
    PDB 1b9x-4l12 »
      4ahx »

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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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

Go back to Gadolinium Binding Sites List in 4ahx
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: Sun Dec 13 18:59:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy