Atomistry » Calcium » PDB 2zp5-3a4h » 2zzv
Atomistry »
  Calcium »
    PDB 2zp5-3a4h »
      2zzv »

Calcium in PDB 2zzv: Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate

Protein crystallography data

The structure of Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate, PDB code: 2zzv was solved by N.Akiyama, K.Takeda, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.33 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.052, 77.335, 136.389, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate (pdb code 2zzv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate, PDB code: 2zzv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2zzv

Go back to Calcium Binding Sites List in 2zzv
Calcium binding site 1 out of 2 in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate


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 A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:10.9
occ:1.00
O A:PHE217 2.3 12.2 1.0
OD1 A:ASN158 2.3 9.3 1.0
O2 A:LAC401 2.4 11.5 1.0
O1 A:LAC401 2.4 9.8 1.0
OE1 A:GLN247 2.4 9.7 1.0
OD2 A:ASP216 2.4 12.7 1.0
OD1 A:ASP216 2.6 12.5 1.0
CG A:ASP216 2.8 11.5 1.0
C1 A:LAC401 3.2 9.9 1.0
CG A:ASN158 3.2 8.7 1.0
CD A:GLN247 3.2 9.7 1.0
C2 A:LAC401 3.3 10.7 1.0
C A:PHE217 3.4 10.2 1.0
NE2 A:GLN247 3.6 9.6 1.0
CB A:ASN158 3.8 9.2 1.0
CA A:PHE217 3.9 9.8 1.0
N A:PHE217 4.1 11.2 1.0
ND2 A:ASN158 4.2 8.4 1.0
C3 A:LAC401 4.2 12.6 1.0
CD A:PRO180 4.3 9.5 1.0
CG A:PRO180 4.3 10.1 1.0
OD2 A:ASP250 4.3 9.4 1.0
CB A:ASP216 4.4 11.6 1.0
NH1 A:ARG178 4.4 9.4 1.0
OXT A:LAC401 4.4 10.2 1.0
CG A:GLN247 4.5 8.9 1.0
C A:ASP216 4.5 11.5 1.0
N A:VAL218 4.6 8.7 1.0
CB A:GLN247 4.7 8.5 1.0
NE2 A:HIS246 4.8 13.7 1.0
CG A:ASP250 4.8 7.9 1.0
CA A:VAL218 4.8 9.6 1.0
O A:ASP216 5.0 11.9 1.0
CD2 A:HIS246 5.0 14.3 1.0
CB A:PRO180 5.0 9.6 1.0

Calcium binding site 2 out of 2 in 2zzv

Go back to Calcium Binding Sites List in 2zzv
Calcium binding site 2 out of 2 in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate


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 A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:13.3
occ:1.00
OD1 B:ASN1158 2.3 11.4 1.0
O B:PHE1217 2.3 12.5 1.0
OE1 B:GLN1247 2.3 12.8 1.0
O1 B:LAC402 2.4 12.3 1.0
OD1 B:ASP1216 2.4 13.8 1.0
O2 B:LAC402 2.4 14.4 1.0
OD2 B:ASP1216 2.6 15.2 1.0
CG B:ASP1216 2.9 13.7 1.0
C1 B:LAC402 3.2 10.5 1.0
CG B:ASN1158 3.2 10.4 1.0
CD B:GLN1247 3.2 11.5 1.0
C2 B:LAC402 3.4 11.4 1.0
C B:PHE1217 3.4 13.5 1.0
NE2 B:GLN1247 3.7 10.8 1.0
CB B:ASN1158 3.8 9.4 1.0
CA B:PHE1217 3.9 12.1 1.0
N B:PHE1217 4.1 13.5 1.0
ND2 B:ASN1158 4.2 11.1 1.0
CD B:PRO1180 4.2 12.0 1.0
CG B:PRO1180 4.2 13.9 1.0
C3 B:LAC402 4.3 14.7 1.0
OD2 B:ASP1250 4.4 12.1 1.0
CB B:ASP1216 4.4 14.1 1.0
NH1 B:ARG1178 4.4 12.8 1.0
CG B:GLN1247 4.4 11.2 1.0
OXT B:LAC402 4.4 14.6 1.0
C B:ASP1216 4.5 14.3 1.0
N B:VAL1218 4.5 12.1 1.0
NE2 B:HIS1246 4.7 15.9 1.0
CB B:GLN1247 4.8 11.8 1.0
CA B:VAL1218 4.8 11.6 1.0
CG B:ASP1250 4.8 11.1 1.0
O B:ASP1216 4.9 14.6 1.0
CD2 B:HIS1246 5.0 15.1 1.0

Reference:

N.Akiyama, K.Takeda, K.Miki. Crystal Structure of A Periplasmic Substrate-Binding Protein in Complex with Calcium Lactate J.Mol.Biol. V. 392 559 2009.
ISSN: ISSN 0022-2836
PubMed: 19631222
DOI: 10.1016/J.JMB.2009.07.043
Page generated: Tue Jul 8 10:18:53 2025

Last articles

Ca in 3A6O
Ca in 3A5N
Ca in 3A5O
Ca in 3A5M
Ca in 3A5L
Ca in 3A4Z
Ca in 3A50
Ca in 3A51
Ca in 3A4U
Ca in 3A3O
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy