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Zinc in PDB 5vh5: Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab

Protein crystallography data

The structure of Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab, PDB code: 5vh5 was solved by S.J.Mayclin, T.E.Edwards, T.F.Lerch, H.Conlan, P.Sharpe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 50.160, 148.030, 75.900, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab (pdb code 5vh5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab, PDB code: 5vh5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5vh5

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Zinc binding site 1 out of 3 in the Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.1
occ:1.00
NE2 A:HIS313 2.0 24.9 1.0
O A:ACT504 2.0 31.9 1.0
NE2 A:HIS438 2.1 19.0 1.0
O A:HOH630 2.1 29.9 1.0
OXT A:ACT504 2.3 43.7 1.0
C A:ACT504 2.4 40.9 1.0
O A:HOH752 2.9 32.5 1.0
CE1 A:HIS313 3.0 21.0 1.0
CD2 A:HIS438 3.0 22.0 1.0
CD2 A:HIS313 3.0 22.1 1.0
CE1 A:HIS438 3.1 22.0 1.0
CH3 A:ACT504 3.6 41.6 1.0
CD1 A:LEU317 3.8 24.5 1.0
ND1 A:HIS313 4.1 20.6 1.0
CG A:HIS313 4.2 24.1 1.0
CG A:HIS438 4.2 19.3 1.0
ND1 A:HIS438 4.2 18.3 1.0

Zinc binding site 2 out of 3 in 5vh5

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Zinc binding site 2 out of 3 in the Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:35.7
occ:0.67
O A:HOH754 1.8 35.5 1.0
ND1 A:HIS288 2.2 45.6 1.0
CG A:HIS288 3.2 45.2 1.0
CE1 A:HIS288 3.2 47.1 1.0
CB A:HIS288 3.4 47.8 1.0
CA A:HIS288 3.9 45.7 1.0
O A:HOH626 4.0 35.3 1.0
NE2 A:HIS288 4.3 44.8 1.0
CD2 A:HIS288 4.3 44.4 1.0
O A:VAL287 4.6 45.1 1.0
OE1 A:GLU286 4.7 45.8 1.0
O A:HIS288 4.7 44.4 1.0
C A:HIS288 4.8 46.4 1.0
N A:HIS288 5.0 41.3 1.0

Zinc binding site 3 out of 3 in 5vh5

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Zinc binding site 3 out of 3 in the Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fc Fragment of Anti-Tnfa Antibody Infliximab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:75.6
occ:0.50
OE2 A:GLU321 2.1 90.3 1.0
OE1 A:GLU321 2.3 85.5 1.0
CD A:GLU321 2.5 81.7 1.0
O A:HOH732 2.9 58.4 1.0
CG A:GLU321 4.0 59.2 1.0
O A:HOH764 4.7 48.1 1.0
CB A:GLU321 4.7 32.9 1.0
O A:HOH604 4.7 37.0 1.0

Reference:

T.F.Lerch, P.Sharpe, S.J.Mayclin, T.E.Edwards, E.Lee, H.D.Conlon, S.Polleck, J.C.Rouse, Y.Luo, Q.Zou. Infliximab Crystal Structures Reveal Insights Into Self-Association. Mabs V. 9 874 2017.
ISSN: ESSN 1942-0870
PubMed: 28421849
DOI: 10.1080/19420862.2017.1320463
Page generated: Wed Dec 16 11:09:22 2020

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