Zinc in PDB 3m7p: Fibronectin Fragment

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

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 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 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 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 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 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 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 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

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