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Zinc in PDB 2xzq: Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf

Protein crystallography data

The structure of Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf, PDB code: 2xzq was solved by T.Khan, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.920, 65.280, 113.560, 90.00, 90.19, 90.00
R / Rfree (%) 24.07 / 25.06

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf (pdb code 2xzq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf, PDB code: 2xzq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2xzq

Go back to Zinc Binding Sites List in 2xzq
Zinc binding site 1 out of 2 in the Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1221

b:32.0
occ:1.00
NE2 H:GLN39 3.1 30.7 1.0
CA H:GLY44 3.5 33.3 1.0
N H:GLY44 3.8 36.3 1.0
CG H:GLN39 3.9 28.6 1.0
CD H:GLN39 3.9 31.1 1.0
CZ L:PHE89 4.0 15.3 1.0
O L:HOH2010 4.0 33.6 1.0
C H:GLY44 4.1 31.5 1.0
CA H:PRO41 4.3 39.5 1.0
O H:GLY44 4.5 30.8 1.0
CD2 H:LEU45 4.5 28.9 1.0
CE1 L:PHE89 4.6 14.0 1.0
N H:LEU45 4.7 29.1 1.0
N H:GLY42 4.8 40.9 1.0
N H:PRO41 4.8 39.0 1.0
O H:ARG40 4.8 38.3 1.0
CG H:LEU45 4.9 26.9 1.0
OE1 H:GLN39 5.0 29.2 1.0

Zinc binding site 2 out of 2 in 2xzq

Go back to Zinc Binding Sites List in 2xzq
Zinc binding site 2 out of 2 in the Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the Anti-(4-Hydroxy-3- Nitrophenyl)-Acetyl Murine Germline Monoclonal Antibody BBE6.12H3 Fab Fragment in Complex with A Phage Display Derived Dodecapeptide Yqlrpnaetlrf within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1221

b:17.4
occ:1.00
C P:THR9 3.2 74.2 1.0
O P:GLU8 3.3 73.6 1.0
CD H:ARG50 3.5 26.3 1.0
O P:THR9 3.7 28.2 1.0
CE1 H:HIS35 3.7 24.4 1.0
CH2 L:TRP93 4.0 19.8 1.0
NE2 H:HIS35 4.1 24.3 1.0
NH1 H:ARG50 4.1 21.2 1.0
CB H:ARG50 4.1 20.2 1.0
CZ3 L:TRP93 4.1 19.9 1.0
CZ3 H:TRP33 4.1 27.6 1.0
C P:GLU8 4.2 73.6 1.0
CG H:ARG50 4.3 22.1 1.0
CZ2 H:TRP47 4.3 16.6 1.0
CE3 H:TRP33 4.4 28.9 1.0
CA P:THR9 4.4 73.8 1.0
NE1 L:TRP98 4.5 15.1 1.0
CB H:ALA59 4.6 20.0 1.0
NE H:ARG50 4.6 26.0 1.0
N P:THR9 4.6 73.7 1.0
OE1 P:GLU8 4.7 72.8 1.0
CD P:GLU8 4.8 70.9 1.0
ND1 H:HIS35 4.8 24.1 1.0
CZ2 L:TRP93 4.8 21.2 1.0
CZ H:ARG50 4.8 26.4 1.0
CD1 L:TRP98 4.9 14.3 1.0
CH2 H:TRP47 5.0 14.9 1.0

Reference:

T.Khan, D.M.Salunke. Structural Elucidation of the Mechanistic Basis of Degeneracy in the Primary Humoral Response. J.Immunol. V. 188 1819 2012.
ISSN: ISSN 0022-1767
PubMed: 22266283
DOI: 10.4049/JIMMUNOL.1102701
Page generated: Thu Oct 17 05:37:32 2024

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