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Manganese in PDB 4mmz: Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin

Protein crystallography data

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin, PDB code: 4mmz was solved by J.Van Agthoven, J.Xiong, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.48 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.790, 129.790, 307.676, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 25.6

Other elements in 4mmz:

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin (pdb code 4mmz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin, PDB code: 4mmz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4mmz

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Manganese binding site 1 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1018

b:0.6
occ:1.00
 OD1 A:ASP238 2.1 0.9 1.0
OD1 A:ASP234 2.1 0.9 1.0
OD2 A:ASP234 2.1 0.4 1.0
OD1 A:ASN232 2.2 1.0 1.0
OD1 A:ASP230 2.2 88.3 1.0
OD2 A:ASP238 2.2 0.1 1.0
CG A:ASP234 2.4 0.5 1.0
CG A:ASP238 2.4 0.7 1.0
O A:ILE236 2.5 86.0 1.0
CG A:ASN232 3.3 97.7 1.0
CG A:ASP230 3.4 92.8 1.0
C A:ILE236 3.7 92.0 1.0
ND2 A:ASN232 3.8 92.3 1.0
O A:ASN232 3.9 0.7 1.0
CB A:ASP234 3.9 98.6 1.0
CB A:ASP238 4.0 82.3 1.0
CA A:ASP230 4.0 85.5 1.0
N A:ILE236 4.1 98.3 1.0
CB A:ASP230 4.2 86.0 1.0
OD2 A:ASP230 4.3 96.9 1.0
N A:ASN232 4.3 0.5 1.0
N A:PHE231 4.3 92.2 1.0
CA A:ILE236 4.4 0.5 1.0
N A:GLY235 4.5 92.9 1.0
N A:ASP238 4.5 95.1 1.0
C A:ASN232 4.5 0.8 1.0
CB A:ASN232 4.6 0.2 1.0
C A:ASP230 4.6 92.2 1.0
N A:ASP234 4.6 0.5 1.0
OD1 A:ASP257 4.6 96.3 1.0
CA A:ASN232 4.7 0.4 1.0
C A:ASP237 4.7 92.1 1.0
CA A:ASP234 4.7 0.9 1.0
CB A:ILE236 4.7 98.1 1.0
CA A:ASP238 4.7 79.6 1.0
N A:ASP237 4.8 96.0 1.0
O A:GLY229 4.8 77.4 1.0
C A:GLY235 5.0 98.8 1.0

Manganese binding site 2 out of 8 in 4mmz

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Manganese binding site 2 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1019

b:0.4
occ:1.00
 O A:TYR290 2.1 0.0 1.0
OD1 A:ASP284 2.1 0.0 1.0
OD1 A:ASP292 2.2 99.9 1.0
OD2 A:ASP292 2.2 0.9 1.0
OD1 A:ASN286 2.2 0.0 1.0
OD1 A:ASP288 2.2 0.8 1.0
CG A:ASP292 2.4 97.2 1.0
CG A:ASN286 3.2 0.2 1.0
C A:TYR290 3.3 0.0 1.0
CG A:ASP288 3.3 0.5 1.0
CG A:ASP284 3.3 0.9 1.0
ND2 A:ASN286 3.5 0.0 1.0
OD2 A:ASP288 3.6 0.6 1.0
CB A:ASP292 3.9 82.8 1.0
CA A:ASP284 4.0 93.4 1.0
CA A:TYR290 4.0 0.8 1.0
CB A:ASP284 4.0 95.6 1.0
N A:TYR290 4.0 0.8 1.0
CB A:TYR290 4.1 0.5 1.0
OD2 A:ASP284 4.3 0.8 1.0
N A:ASP292 4.3 84.1 1.0
N A:ILE285 4.3 92.4 1.0
C A:ALA291 4.3 90.1 1.0
N A:ALA291 4.3 98.9 1.0
N A:ASP288 4.4 0.1 1.0
N A:ASN286 4.4 96.9 1.0
C A:ASP284 4.5 0.1 1.0
N A:ASP289 4.6 0.5 1.0
CB A:ASN286 4.6 0.8 1.0
CB A:ASP288 4.6 0.9 1.0
CA A:ASP292 4.6 81.3 1.0
CA A:ALA291 4.6 91.7 1.0
O A:ALA291 4.7 95.1 1.0
O A:GLN320 4.7 0.3 1.0
C A:ASP288 4.7 0.3 1.0
CA A:ASP288 4.8 0.8 1.0
N A:GLN320 4.9 0.0 1.0
O A:THR283 4.9 0.4 1.0
CA A:ASN286 4.9 0.6 1.0
N A:GLY287 5.0 99.2 1.0

Manganese binding site 3 out of 8 in 4mmz

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Manganese binding site 3 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1020

b:0.3
occ:1.00
 OD1 A:ASP349 2.1 0.3 1.0
OD1 A:ASP353 2.2 0.3 1.0
OD1 A:ASP357 2.2 0.1 1.0
OD1 A:ASP351 2.2 0.3 1.0
OD2 A:ASP357 2.2 0.9 1.0
O A:PHE355 2.3 0.1 1.0
CG A:ASP357 2.5 0.3 1.0
CG A:ASP351 3.2 0.1 1.0
CG A:ASP353 3.3 0.6 1.0
CG A:ASP349 3.4 0.9 1.0
C A:PHE355 3.5 0.2 1.0
OD2 A:ASP351 3.6 0.2 1.0
OD2 A:ASP353 3.9 0.7 1.0
CB A:ASP357 4.0 88.5 1.0
N A:LEU350 4.1 90.4 1.0
OD2 A:ASP349 4.1 0.4 1.0
N A:ASP351 4.1 99.5 1.0
C A:ASN356 4.1 86.0 1.0
O A:ASN356 4.3 0.2 1.0
N A:ASP357 4.3 85.9 1.0
CA A:ASP349 4.4 90.0 1.0
CA A:PHE355 4.4 0.3 1.0
N A:PHE355 4.4 0.3 1.0
N A:GLY378 4.4 0.5 1.0
CB A:ASP349 4.4 90.9 1.0
C A:ASP349 4.4 89.0 1.0
N A:ASN356 4.5 94.1 1.0
CB A:ASP353 4.5 94.9 1.0
CB A:ASP351 4.5 91.0 1.0
CA A:ASN356 4.5 88.3 1.0
N A:ASP353 4.6 90.5 1.0
OD1 A:ASN377 4.6 76.8 1.0
CB A:PHE355 4.6 0.3 1.0
O A:GLY378 4.6 0.3 1.0
CA A:ASP357 4.6 0.2 1.0
CA A:ASP351 4.8 0.8 1.0
N A:GLN352 4.8 82.4 1.0
CG A:ASN377 4.9 87.8 1.0
CB A:ASN377 4.9 78.2 1.0
CA A:LEU350 5.0 80.2 1.0
CA A:ASN377 5.0 78.7 1.0

Manganese binding site 4 out of 8 in 4mmz

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Manganese binding site 4 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1021

b:0.1
occ:1.00
 O A:TYR419 2.1 83.1 1.0
OD1 A:ASP415 2.2 0.6 1.0
OD1 A:ASP421 2.2 0.1 1.0
OD2 A:ASP421 2.2 0.2 1.0
OD1 A:ASN417 2.2 0.2 1.0
OD1 A:ASP413 2.3 0.4 1.0
CG A:ASP421 2.5 0.5 1.0
ND2 A:ASN417 2.5 1.0 1.0
CG A:ASN417 2.7 0.9 1.0
CG A:ASP415 3.3 0.4 1.0
C A:TYR419 3.3 82.1 1.0
CG A:ASP413 3.4 0.7 1.0
OD2 A:ASP415 3.7 0.6 1.0
CB A:ASP421 4.0 80.8 1.0
N A:TYR419 4.0 87.7 1.0
CA A:TYR419 4.1 83.7 1.0
OD2 A:ASP413 4.1 93.3 1.0
O A:ASP415 4.1 0.9 1.0
CB A:ASN417 4.2 0.1 1.0
C A:PRO420 4.2 77.8 1.0
N A:PRO420 4.3 80.8 1.0
N A:ASP421 4.3 80.6 1.0
N A:ASP415 4.3 93.9 1.0
CB A:TYR419 4.3 0.1 1.0
CA A:ASP413 4.3 85.9 1.0
CB A:ASP413 4.4 88.4 1.0
O A:ALA437 4.4 0.1 1.0
N A:ALA437 4.4 92.4 1.0
N A:ILE414 4.4 87.5 1.0
CA A:PRO420 4.5 78.1 1.0
O A:PRO420 4.6 87.0 1.0
CB A:ASP415 4.6 98.5 1.0
CA A:ASP421 4.6 82.8 1.0
C A:ASP415 4.7 1.0 1.0
C A:ASP413 4.7 91.0 1.0
CB A:ALA437 4.7 77.1 1.0
CA A:ASP415 4.8 97.9 1.0
N A:ASN417 4.8 0.8 1.0
N A:GLY418 4.9 95.6 1.0
CA A:ASN417 4.9 0.3 1.0

Manganese binding site 5 out of 8 in 4mmz

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Manganese binding site 5 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1022

b:0.4
occ:1.00
 OD1 A:ASP599 2.1 0.3 1.0
OE1 A:GLU636 2.1 0.5 1.0
OE2 A:GLU636 2.2 0.2 1.0
OD2 A:ASP599 2.2 0.3 1.0
O A:VAL601 2.2 0.5 1.0
CD A:GLU636 2.4 0.1 1.0
O A:CYS596 2.4 1.0 1.0
CG A:ASP599 2.4 0.7 1.0
C A:VAL601 3.5 0.8 1.0
C A:CYS596 3.6 0.6 1.0
CG A:GLU636 3.9 0.6 1.0
CB A:ASP599 4.0 0.9 1.0
N A:LYS603 4.2 97.5 1.0
N A:VAL601 4.2 0.8 1.0
CE A:LYS603 4.3 0.4 1.0
CG2 A:VAL601 4.3 0.5 1.0
CA A:CYS602 4.3 86.8 1.0
N A:CYS602 4.4 0.9 1.0
CA A:GLY597 4.4 0.2 1.0
CA A:VAL601 4.4 0.3 1.0
N A:GLY597 4.4 0.3 1.0
CA A:CYS596 4.6 0.7 1.0
N A:ASP599 4.7 0.2 1.0
CB A:GLU636 4.7 0.8 1.0
C A:CYS602 4.7 0.1 1.0
CA A:ASP599 4.8 0.9 1.0
CB A:LYS603 4.9 0.2 1.0
C A:GLY597 4.9 0.3 1.0
CG A:LYS603 4.9 0.1 1.0
N A:ASN600 4.9 0.1 1.0
CB A:CYS596 4.9 0.6 1.0
CB A:VAL601 5.0 0.3 1.0

Manganese binding site 6 out of 8 in 4mmz

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Manganese binding site 6 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn708

b:73.4
occ:1.00
 OE1 B:GLU220 2.2 0.9 1.0
OD1 C:ASP1495 2.2 89.2 1.0
O B:HOH801 2.2 0.2 1.0
O B:HOH802 2.2 46.0 1.0
OG B:SER121 2.2 85.7 1.0
O C:HOH1701 2.2 75.0 1.0
CB B:SER121 2.8 79.1 1.0
CD B:GLU220 2.9 88.1 1.0
CG B:GLU220 2.9 78.2 1.0
CG C:ASP1495 3.1 89.9 1.0
OD2 C:ASP1495 3.8 80.5 1.0
O C:HOH1705 3.8 0.7 1.0
CB C:ASP1495 3.9 69.8 1.0
OD2 B:ASP119 4.0 90.0 1.0
OE2 B:GLU220 4.1 96.7 1.0
CA B:SER121 4.2 85.1 1.0
CA C:ASP1495 4.3 70.1 1.0
CB B:GLU220 4.3 80.1 1.0
O B:ALA218 4.3 86.4 1.0
OD1 B:ASP119 4.4 0.7 1.0
CG B:ASP119 4.6 0.3 1.0
C B:SER121 4.7 0.1 1.0
CB B:ALA252 4.9 0.1 1.0
OD1 B:ASP251 4.9 85.8 1.0
C C:ASP1495 5.0 83.7 1.0
N B:SER121 5.0 82.9 1.0

Manganese binding site 7 out of 8 in 4mmz

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Manganese binding site 7 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn709

b:99.8
occ:1.00
 OD1 B:ASP127 2.1 0.8 1.0
OD1 B:ASP126 2.1 0.7 1.0
OD2 B:ASP126 2.2 0.5 1.0
O B:SER123 2.2 0.6 1.0
O C:HOH1702 2.2 0.8 1.0
CG B:ASP126 2.5 0.1 1.0
O B:MET335 2.6 97.3 1.0
CG B:ASP127 3.2 0.4 1.0
C B:SER123 3.4 0.0 1.0
CE B:MET124 3.4 0.7 1.0
OD2 B:ASP127 3.6 0.6 1.0
C B:MET335 3.7 0.6 1.0
CA B:MET124 3.9 96.6 1.0
CB B:ASP126 4.0 97.4 1.0
N B:MET124 4.1 0.3 1.0
OG B:SER123 4.2 0.6 1.0
N B:ASP127 4.4 0.1 1.0
CA B:MET335 4.5 0.3 1.0
CB B:ASP127 4.5 0.9 1.0
C B:MET124 4.5 0.8 1.0
CA B:SER123 4.5 95.1 1.0
OH C:TYR1446 4.6 0.9 1.0
N B:ASP126 4.7 0.2 1.0
N B:ASP336 4.7 0.6 1.0
CA B:ASP126 4.8 0.3 1.0
CB B:SER123 4.8 91.7 1.0
CA B:ASP336 4.8 0.8 1.0
CB B:MET335 4.9 0.4 1.0
SD B:MET124 4.9 0.1 1.0
C B:ASP126 5.0 0.9 1.0
N B:LYS125 5.0 0.9 1.0

Manganese binding site 8 out of 8 in 4mmz

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Manganese binding site 8 out of 8 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn710

b:0.3
occ:1.00
 O B:PRO219 2.1 67.8 1.0
OD1 B:ASP217 2.2 95.9 1.0
OE2 B:GLU220 2.2 96.7 1.0
OD2 B:ASP158 2.2 70.1 1.0
O B:ASP217 2.2 75.2 1.0
OD1 B:ASN215 2.2 73.2 1.0
CG B:ASP217 3.1 75.1 1.0
C B:PRO219 3.1 89.1 1.0
CD B:GLU220 3.2 88.1 1.0
C B:ASP217 3.3 74.0 1.0
CG B:ASP158 3.4 72.3 1.0
CG B:ASN215 3.4 80.2 1.0
OD2 B:ASP217 3.6 87.9 1.0
CA B:GLU220 3.7 81.7 1.0
N B:GLU220 3.8 76.1 1.0
NE2 B:HIS255 4.0 63.8 1.0
CB B:ASP158 4.0 69.7 1.0
N B:PRO219 4.0 74.1 1.0
CG B:GLU220 4.0 78.2 1.0
C B:ALA218 4.0 74.0 1.0
OE1 B:GLU220 4.0 0.9 1.0
CA B:ASP217 4.1 76.3 1.0
CB B:ASP217 4.1 71.2 1.0
CA B:PRO219 4.1 75.5 1.0
O B:ALA218 4.2 86.4 1.0
N B:ASP217 4.2 87.8 1.0
ND2 B:ASN215 4.2 0.9 1.0
CB B:GLU220 4.3 80.1 1.0
N B:ALA218 4.3 87.8 1.0
CD2 B:HIS255 4.3 64.1 1.0
OD1 B:ASP158 4.4 65.8 1.0
CB B:ASN215 4.4 81.2 1.0
CA B:ALA218 4.6 79.4 1.0
CD B:PRO219 4.7 1.0 1.0
CB B:PRO219 4.9 72.4 1.0
CD1 B:TYR164 4.9 83.9 1.0
CB B:TYR164 5.0 81.3 1.0
C B:GLU220 5.0 81.2 1.0

Reference:

J.F.Van Agthoven, J.P.Xiong, J.L.Alonso, X.Rui, B.D.Adair, S.L.Goodman, M.A.Arnaout. Structural Basis For Pure Antagonism of Integrin Alpha V Beta 3 By A High-Affinity Form of Fibronectin. Nat.Struct.Mol.Biol. V. 21 383 2014.
ISSN: ISSN 1545-9993
PubMed: 24658351
DOI: 10.1038/NSMB.2797
Page generated: Tue Dec 15 04:24:37 2020

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