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Calcium in PDB 3s35: Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies

Enzymatic activity of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies

All present enzymatic activity of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies:
2.7.10.1;

Protein crystallography data

The structure of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies, PDB code: 3s35 was solved by M.C.Franklin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.79 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.937, 112.130, 156.971, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies (pdb code 3s35). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies, PDB code: 3s35:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 1 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca218

b:6.8
occ:1.00
 OD2 H:ASP100 2.3 17.4 1.0
OD2 H:ASP105 2.4 10.5 1.0
O X:HOH161 2.7 27.8 1.0
O H:HOH346 2.9 20.5 1.0
CG H:ASP100 3.2 15.6 1.0
CG H:ASP105 3.4 11.5 1.0
CB H:ASP100 3.4 11.6 1.0
CB H:ASP105 3.6 12.5 1.0
NZ X:LYS271 3.7 31.2 1.0
NH2 H:ARG98 4.1 6.1 1.0
CE X:LYS271 4.3 30.0 1.0
OD1 H:ASP100 4.4 16.2 1.0
OD1 H:ASP105 4.5 8.3 1.0
O X:LYS266 4.9 29.4 1.0
CA H:ASP100 5.0 11.3 1.0

Calcium binding site 2 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 2 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca219

b:57.4
occ:1.00
 OD2 H:ASP66 2.0 31.4 1.0
O H:HOH265 2.5 33.4 1.0
CG H:ASP66 3.1 28.7 1.0
OD1 H:ASP66 3.5 31.2 1.0
O H:HOH273 4.3 56.8 1.0
CB H:ASP66 4.3 23.9 1.0

Calcium binding site 3 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 3 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca218

b:59.1
occ:1.00
 O L:HOH298 2.4 34.0 1.0
OE2 L:GLU27 2.4 35.6 1.0
N L:ASP1 2.5 33.3 1.0
OE2 L:GLU97 2.9 37.5 1.0
CD L:GLU27 3.5 31.6 1.0
CD L:GLU97 3.6 33.3 1.0
CA L:ASP1 3.9 30.9 1.0
OE1 L:GLU27 4.0 36.8 1.0
O L:HOH373 4.0 40.7 1.0
OE1 L:GLU97 4.1 34.9 1.0
CG L:GLU97 4.6 27.4 1.0
C L:ASP1 4.6 28.8 1.0
CG1 L:ILE2 4.7 22.3 1.0
CG L:GLU27 4.8 29.4 1.0
CB L:ASP1 5.0 32.7 1.0

Calcium binding site 4 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 4 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca219

b:21.5
occ:1.00
 OD2 L:ASP98 2.1 25.6 1.0
O L:HOH259 2.4 21.6 1.0
O L:HOH224 2.4 25.0 1.0
O L:HOH227 2.7 7.4 1.0
CG L:ASP98 3.1 23.4 1.0
OD1 L:ASP98 3.5 26.7 1.0
O X:GLY239 3.9 18.0 1.0
NE1 H:TRP50 4.2 11.4 1.0
CB L:ASP98 4.4 22.6 1.0
NZ H:LYS59 4.5 30.5 1.0
O H:HOH238 4.6 28.3 1.0
O L:HOH285 4.7 25.9 1.0
CD2 L:LEU100 4.8 13.8 1.0
C X:GLY239 4.8 17.2 1.0
CD1 H:TRP50 4.9 10.1 1.0

Calcium binding site 5 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 5 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca1

b:3.4
occ:1.00
 O X:HOH363 1.3 2.0 1.0
O X:HOH181 2.3 20.6 1.0
OE1 X:GLU251 2.5 24.7 1.0
O X:HOH345 2.7 40.9 1.0
OE2 X:GLU251 3.2 26.9 1.0
CD X:GLU251 3.2 24.5 1.0
N X:GLY220 3.9 27.1 1.0
N X:TYR221 4.0 25.3 1.0
CG X:PRO219 4.1 29.1 1.0
CB X:ARG222 4.1 23.8 1.0
N X:ARG222 4.2 23.0 1.0
CA X:GLY220 4.3 26.3 1.0
C X:GLY220 4.6 25.0 1.0
CG X:GLU251 4.7 20.9 1.0
CB X:PRO219 4.7 29.1 1.0
CA X:ARG222 4.8 21.9 1.0
CD X:PRO219 4.8 30.9 1.0
CG X:ARG222 4.9 26.5 1.0
C X:PRO219 5.0 27.6 1.0

Calcium binding site 6 out of 6 in 3s35

Go back to Calcium Binding Sites List in 3s35
Calcium binding site 6 out of 6 in the Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Basis For the Function of Two Anti-Vegf Receptor Antibodies within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca2

b:8.7
occ:1.00
 O X:HOH364 1.3 4.0 1.0
O X:HOH189 2.4 24.4 1.0
OE1 X:GLU235 2.6 40.5 1.0
OE2 X:GLU235 2.6 39.9 1.0
CD X:GLU235 2.9 37.1 1.0
CG X:GLU235 4.2 31.8 1.0
NE2 X:HIS325 4.5 36.8 1.0
CE1 X:HIS325 4.6 37.4 1.0

Reference:

M.C.Franklin, E.C.Navarro, Y.Wang, S.Patel, P.Singh, Y.Zhang, K.Persaud, A.Bari, H.Griffith, L.Shen, P.Balderes, P.Kussie. The Structural Basis For the Function of Two Anti-Vegf Receptor 2 Antibodies. Structure V. 19 1097 2011.
ISSN: ISSN 0969-2126
PubMed: 21827946
DOI: 10.1016/J.STR.2011.01.019
Page generated: Tue Jul 8 16:28:49 2025

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