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Calcium in PDB 4jo2: Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120

Protein crystallography data

The structure of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120, PDB code: 4jo2 was solved by R.M.Pan, X.P.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.47 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.840, 74.350, 84.960, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 (pdb code 4jo2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120, PDB code: 4jo2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4jo2

Go back to Calcium Binding Sites List in 4jo2
Calcium binding site 1 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca301

b:16.9
occ:1.00
 N L:PHE98 3.3 8.2 1.0
N H:TRP47 3.4 11.0 1.0
O L:HOH422 3.5 18.9 1.0
O H:HOH495 3.7 6.8 1.0
CA L:ALA97 3.8 10.1 1.0
CB L:PHE98 4.0 11.0 1.0
CA H:GLU46 4.0 12.2 1.0
CD2 L:PHE98 4.0 8.6 1.0
CB H:TRP47 4.0 9.1 1.0
C L:ALA97 4.1 8.7 1.0
CA L:PHE98 4.2 8.6 1.0
C H:GLU46 4.2 9.8 1.0
O H:LEU45 4.3 12.3 1.0
CA H:TRP47 4.3 9.5 1.0
CG H:GLU46 4.3 8.9 1.0
CG L:PHE98 4.5 9.8 1.0
O L:PHE98 4.5 8.6 1.0
CB L:ALA97 4.5 9.1 1.0
O L:ALA96 4.6 11.6 1.0
CB H:GLU46 4.7 9.0 1.0
O L:HOH413 4.7 11.9 1.0
O H:TRP47 4.8 7.2 1.0
N L:ALA97 4.8 8.6 1.0
C L:PHE98 4.9 7.5 1.0
N H:GLU46 5.0 8.4 1.0
C H:LEU45 5.0 7.7 1.0

Calcium binding site 2 out of 6 in 4jo2

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Calcium binding site 2 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca302

b:37.5
occ:1.00
 N L:SER9 3.3 15.4 1.0
CA L:PRO8 3.7 15.3 1.0
C L:PRO8 4.0 15.3 1.0
CB L:SER9 4.1 12.7 1.0
CB L:PRO8 4.1 16.8 1.0
CA L:SER9 4.3 12.9 1.0
OG L:SER9 4.3 22.7 1.0
CG2 L:THR7 4.4 22.0 1.0
CB L:THR7 4.5 17.9 1.0
CA L:THR7 4.9 14.8 1.0
N L:PRO8 5.0 14.4 1.0

Calcium binding site 3 out of 6 in 4jo2

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Calcium binding site 3 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:29.6
occ:1.00
 O H:HOH491 3.2 6.7 1.0
N H:TYR59 3.4 11.7 1.0
O H:HOH454 3.5 18.2 1.0
O H:HOH452 3.8 21.3 1.0
O L:HOH475 3.8 23.7 1.0
CA H:ALA58 3.9 8.9 1.0
CD1 H:TYR59 3.9 6.7 1.0
CD H:LYS64 4.0 10.8 1.0
O H:TYR59 4.1 10.7 1.0
C H:ALA58 4.2 10.6 1.0
CB H:TYR59 4.3 10.1 1.0
CA H:TYR59 4.3 9.5 1.0
CB H:ALA58 4.5 10.5 1.0
CG H:LYS64 4.5 10.6 1.0
O H:ALA57 4.6 8.5 1.0
CE H:LYS64 4.6 14.9 1.0
CG H:TYR59 4.6 8.4 1.0
NZ H:LYS64 4.6 13.6 1.0
C H:TYR59 4.6 9.0 1.0
O H:HOH403 4.7 19.7 1.0
CE1 H:TYR59 4.9 6.3 1.0
N H:ALA58 5.0 13.2 1.0

Calcium binding site 4 out of 6 in 4jo2

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Calcium binding site 4 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca301

b:13.8
occ:1.00
 N I:TRP47 3.2 9.5 1.0
O I:HOH427 3.2 11.8 1.0
N M:PHE98 3.3 11.4 1.0
CA M:ALA97 3.8 9.8 1.0
O M:HOH471 3.8 27.4 1.0
CA I:GLU46 3.8 7.5 1.0
CD2 M:PHE98 3.8 8.3 1.0
C I:GLU46 4.0 9.7 1.0
CB M:PHE98 4.0 9.5 1.0
CB I:TRP47 4.0 9.2 1.0
O M:HOH482 4.0 15.6 1.0
C M:ALA97 4.0 12.8 1.0
CA I:TRP47 4.2 7.7 1.0
O I:HOH420 4.2 12.9 1.0
CA M:PHE98 4.2 11.2 1.0
O I:HOH440 4.3 19.9 1.0
CG M:PHE98 4.4 10.1 1.0
O I:LEU45 4.4 8.3 1.0
O I:HOH408 4.5 10.0 1.0
CG I:GLU46 4.5 8.4 1.0
CB M:ALA97 4.5 10.8 1.0
O I:TRP47 4.6 10.2 1.0
CB I:GLU46 4.6 7.7 1.0
O M:PHE98 4.7 10.5 1.0
N M:ALA97 4.7 8.5 1.0
O M:ALA96 4.7 10.1 1.0
N I:GLU46 4.8 7.3 1.0
CE2 M:PHE98 4.9 13.0 1.0
C I:TRP47 4.9 10.2 1.0
C M:PHE98 5.0 11.0 1.0

Calcium binding site 5 out of 6 in 4jo2

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Calcium binding site 5 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca302

b:38.5
occ:1.00
 N M:SER9 3.2 14.0 1.0
OG M:SER9 3.5 27.7 1.0
CA M:PRO8 3.5 18.4 1.0
C M:PRO8 3.8 17.5 1.0
CB M:PRO8 4.1 18.1 1.0
CB M:SER9 4.2 16.2 1.0
CA M:SER9 4.3 16.6 1.0
CB M:THR7 4.4 16.8 1.0
CG2 M:THR7 4.5 22.1 1.0
CA M:THR7 4.7 19.7 1.0
N M:PRO8 4.8 19.6 1.0
O M:PRO8 5.0 16.6 1.0

Calcium binding site 6 out of 6 in 4jo2

Go back to Calcium Binding Sites List in 4jo2
Calcium binding site 6 out of 6 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Consensus A GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:32.1
occ:1.00
 N I:TYR59 3.3 9.9 1.0
O I:HOH443 3.4 15.6 1.0
O I:HOH450 3.7 11.9 1.0
CA I:ALA58 3.8 8.2 1.0
CD1 I:TYR59 3.8 8.3 1.0
C I:ALA58 3.9 7.8 1.0
CB I:TYR59 4.0 7.5 1.0
O I:TYR59 4.0 15.2 1.0
CA I:TYR59 4.1 11.2 1.0
O M:HOH429 4.1 13.9 1.0
CD I:LYS64 4.2 15.2 1.0
CE I:LYS64 4.3 14.2 1.0
CB I:ALA58 4.4 11.4 1.0
CG I:TYR59 4.4 7.5 1.0
CG I:LYS64 4.4 11.4 1.0
C I:TYR59 4.5 11.0 1.0
O I:ALA57 4.6 10.9 1.0
NZ I:LYS64 4.8 19.1 1.0
CE1 I:TYR59 4.9 7.3 1.0
N I:ALA58 4.9 9.1 1.0
O M:HOH404 4.9 11.4 1.0
CB I:LYS64 5.0 9.4 1.0

Reference:

R.Pan, J.M.Sampson, Y.Chen, M.Vaine, S.Wang, S.Lu, X.P.Kong. Rabbit Anti-Hiv-1 Monoclonal Antibodies Raised By Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived From Hiv-1-Infected Humans. J.Virol. V. 87 10221 2013.
ISSN: ISSN 0022-538X
PubMed: 23864637
DOI: 10.1128/JVI.00843-13
Page generated: Tue Jul 8 23:11:15 2025

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