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Zinc in PDB 3m7p: Fibronectin Fragment

Protein crystallography data

The structure of Fibronectin Fragment, PDB code: 3m7p was solved by M.Graille, M.Pagano, T.Rose, M.Reboud Ravaux, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.789, 124.789, 60.649, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Fibronectin Fragment (pdb code 3m7p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Fibronectin Fragment, PDB code: 3m7p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3m7p

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Zinc binding site 1 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn953

b:49.7
occ:1.00
OD1 A:ASP529 1.9 59.0 1.0
OE1 A:GLU467 2.0 39.9 1.0
ND1 A:HIS532 2.1 42.6 1.0
OE2 A:GLU467 2.6 65.8 1.0
CD A:GLU467 2.6 62.3 1.0
CG A:ASP529 2.7 59.1 1.0
CE1 A:HIS532 3.0 41.4 1.0
OD2 A:ASP529 3.0 63.0 1.0
CG A:HIS532 3.2 41.5 1.0
CB A:HIS532 3.6 39.6 1.0
O A:ARG503 3.9 46.1 1.0
CG A:GLU467 4.1 47.5 1.0
NE2 A:HIS532 4.1 41.6 1.0
CB A:ASP529 4.2 48.2 1.0
CD2 A:HIS532 4.2 42.4 1.0
N A:HIS532 4.3 40.2 1.0
C A:ARG503 4.3 44.9 1.0
CA A:ARG503 4.5 41.9 1.0
CA A:HIS532 4.6 39.8 1.0
O A:VAL527 4.8 48.7 1.0
CG A:ARG503 4.8 47.6 1.0
CB A:GLU467 4.8 42.2 1.0
CB A:PHE531 4.8 46.3 1.0

Zinc binding site 2 out of 7 in 3m7p

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Zinc binding site 2 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn954

b:40.6
occ:1.00
NE2 A:HIS535 2.1 34.6 1.0
ND1 A:HIS598 2.2 41.3 1.0
O A:HOH34 2.2 11.1 1.0
CE1 A:HIS535 2.9 34.3 1.0
CG A:HIS598 3.1 39.9 1.0
CD2 A:HIS535 3.2 34.7 1.0
CE1 A:HIS598 3.2 40.1 1.0
CB A:HIS598 3.3 37.2 1.0
NE A:ARG369 3.9 52.6 1.0
ND1 A:HIS535 4.1 34.6 1.0
OD1 A:ASN367 4.1 53.6 1.0
CG A:HIS535 4.2 33.8 1.0
CD2 A:HIS598 4.3 41.0 1.0
NE2 A:HIS598 4.3 40.4 1.0
NH2 A:ARG369 4.4 45.5 1.0
CZ A:ARG369 4.4 51.9 1.0
OE1 A:GLN600 4.5 52.0 1.0
CD A:ARG369 4.6 37.1 1.0
CA A:HIS598 4.8 38.0 1.0

Zinc binding site 3 out of 7 in 3m7p

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Zinc binding site 3 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn956

b:42.6
occ:1.00
NE2 A:HIS383 2.0 38.8 1.0
O A:HOH13 2.0 38.5 1.0
CD2 A:HIS383 2.9 39.5 1.0
CE1 A:HIS383 3.0 38.5 1.0
CB A:ASP381 4.0 38.2 1.0
OD2 A:ASP381 4.0 47.1 1.0
CG A:HIS383 4.1 38.1 1.0
ND1 A:HIS383 4.1 39.2 1.0
CG A:ASP381 4.3 44.5 1.0
C35 A:12P189 4.5 62.3 1.0
C36 A:12P189 4.5 61.7 1.0
O34 A:12P189 4.8 65.1 1.0
O A:ASP381 4.9 44.9 1.0
C33 A:12P189 5.0 64.2 1.0

Zinc binding site 4 out of 7 in 3m7p

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Zinc binding site 4 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn957

b:58.1
occ:1.00
NE2 A:HIS466 1.9 47.8 1.0
OE1 A:GLU468 2.1 53.2 1.0
CD A:GLU468 2.8 65.7 1.0
OE2 A:GLU468 2.8 57.9 1.0
CE1 A:HIS466 2.8 47.7 1.0
CD2 A:HIS466 3.0 48.7 1.0
ND1 A:HIS466 4.0 49.5 1.0
CD1 A:ILE480 4.0 47.0 1.0
CG A:HIS466 4.0 48.3 1.0
O A:HOH31 4.2 48.0 1.0
CG A:GLU468 4.3 49.8 1.0

Zinc binding site 5 out of 7 in 3m7p

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Zinc binding site 5 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn958

b:62.6
occ:1.00
ND1 A:HIS307 2.1 60.1 1.0
ND1 A:HIS299 2.1 68.8 1.0
O A:HOH10 2.2 36.5 1.0
CE1 A:HIS307 2.9 59.6 1.0
CE1 A:HIS299 3.0 67.6 1.0
CG A:HIS307 3.2 58.2 1.0
CG A:HIS299 3.2 68.8 1.0
CB A:HIS299 3.6 68.2 1.0
CB A:HIS307 3.6 54.5 1.0
NE2 A:HIS307 4.1 59.9 1.0
NE2 A:HIS299 4.2 67.9 1.0
CD2 A:HIS307 4.2 60.0 1.0
CD2 A:HIS299 4.3 68.6 1.0
CA A:HIS307 4.9 53.5 1.0
N A:HIS307 5.0 54.2 1.0

Zinc binding site 6 out of 7 in 3m7p

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Zinc binding site 6 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn959

b:67.6
occ:0.50
NE2 A:HIS488 2.0 99.3 1.0
NE2 A:HIS581 2.1 92.6 1.0
OE2 A:GLU474 2.3 71.2 1.0
CD2 A:HIS581 2.4 92.5 1.0
CD2 A:HIS488 2.9 99.7 1.0
CE1 A:HIS488 2.9 99.1 1.0
OE1 A:GLU474 2.9 0.1 1.0
CD A:GLU474 2.9 95.2 1.0
CE1 A:HIS581 3.4 92.2 1.0
CG A:HIS581 3.7 89.7 1.0
CG A:HIS488 3.9 98.0 1.0
ND1 A:HIS488 3.9 99.8 1.0
ND1 A:HIS581 4.1 92.2 1.0
CG A:GLU474 4.4 73.9 1.0
CG A:GLN487 4.8 0.8 1.0
CB A:HIS581 4.9 85.2 1.0

Zinc binding site 7 out of 7 in 3m7p

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Zinc binding site 7 out of 7 in the Fibronectin Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Fibronectin Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn955

b:45.5
occ:1.00
O A:HOH37 1.8 26.5 1.0
O A:HOH39 2.0 30.4 1.0
O A:HOH38 2.1 65.4 1.0
OE2 A:GLU537 2.2 46.4 1.0
O A:HOH40 2.2 44.3 1.0
O A:HOH36 2.2 37.8 1.0
CD A:GLU537 3.2 47.8 1.0
OE1 A:GLU537 3.5 48.8 1.0
NE2 A:HIS539 3.8 39.6 1.0
OE2 A:GLU596 3.9 40.1 1.0
O A:HOH54 4.2 48.2 1.0
CE1 A:HIS539 4.2 39.3 1.0
CD A:GLU596 4.2 55.5 1.0
OE1 A:GLU377 4.3 42.4 1.0
OE1 A:GLU596 4.3 60.3 1.0
O A:HOH12 4.4 49.2 1.0
O A:HOH68 4.4 36.3 1.0
CG A:GLU537 4.5 36.8 1.0
OE2 A:GLU377 4.6 45.8 1.0
CD A:GLU377 4.9 57.9 1.0

Reference:

M.Graille, M.Pagano, T.Rose, M.Reboud Ravaux, H.Van Tilbeurgh. Zinc Induces Structural Reorganization of Gelatin Binding Domain From Human Fibronectin and Affects Collagen Binding Structure V. 18 710 2010.
ISSN: ISSN 0969-2126
PubMed: 20541508
DOI: 10.1016/J.STR.2010.03.012
Page generated: Wed Dec 16 04:34:33 2020

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