Atomistry » Calcium » PDB 3m0c-3mip » 3m8d
Atomistry »
  Calcium »
    PDB 3m0c-3mip »
      3m8d »

Calcium in PDB 3m8d: Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin

Protein crystallography data

The structure of Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin, PDB code: 3m8d was solved by D.M.Freed, P.S.Horanyi, M.C.Wiener, D.S.Cafiso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.04 / 2.44
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.051, 82.051, 224.457, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 27.5

Other elements in 3m8d:

The structure of Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin also contains other interesting chemical elements:

Cobalt (Co) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin (pdb code 3m8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin, PDB code: 3m8d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3m8d

Go back to Calcium Binding Sites List in 3m8d
Calcium binding site 1 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca709

b:75.5
occ:1.00
OD2 A:ASP230 2.0 31.9 1.0
OD1 A:ASP193 2.2 29.0 1.0
OD1 A:ASP179 2.2 27.4 1.0
O A:ASP193 2.5 32.3 1.0
O A:GLN191 2.5 34.1 1.0
OD2 A:ASP195 2.6 33.9 1.0
CG A:ASP230 2.7 31.8 1.0
OD1 A:ASP230 2.8 30.4 1.0
OD1 A:ASP195 3.2 35.0 1.0
CG A:ASP195 3.2 34.1 1.0
CG A:ASP179 3.2 35.2 1.0
CG A:ASP193 3.4 31.1 1.0
C A:ASP193 3.4 33.0 1.0
C A:GLN191 3.5 34.1 1.0
N A:ASP193 3.6 32.2 1.0
C A:THR192 3.8 32.7 1.0
CA A:ASP193 3.9 32.2 1.0
CB A:ASP179 4.0 34.3 1.0
CA A:ASP179 4.1 34.4 1.0
CA A:CA710 4.1 82.8 1.0
N A:THR192 4.1 33.5 1.0
OD2 A:ASP179 4.1 37.0 1.0
CA A:THR192 4.2 32.9 1.0
N A:VAL180 4.2 34.5 1.0
CB A:ASP230 4.2 31.4 1.0
CB A:GLN191 4.3 34.8 1.0
CB A:ASP193 4.3 32.1 1.0
O A:THR192 4.3 33.2 1.0
OD2 A:ASP193 4.3 26.5 1.0
CA A:GLN191 4.5 34.6 1.0
C A:ASP179 4.5 34.5 1.0
N A:ASN194 4.6 33.5 1.0
CB A:ASP195 4.6 33.8 1.0
N A:VAL181 4.7 34.0 1.0
C A:ASN194 4.9 33.8 1.0
N A:ASP195 5.0 33.8 1.0
CG2 A:VAL180 5.0 32.7 1.0

Calcium binding site 2 out of 3 in 3m8d

Go back to Calcium Binding Sites List in 3m8d
Calcium binding site 2 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca710

b:82.8
occ:1.00
OD1 A:ASP230 2.2 30.4 1.0
O A:TYR229 2.3 29.6 1.0
OD1 A:ASP195 2.4 35.0 1.0
OD2 A:ASP193 2.5 26.5 1.0
OD1 A:ASP193 2.9 29.0 1.0
CG A:ASP193 3.1 31.1 1.0
C A:TYR229 3.3 29.9 1.0
CG A:ASP230 3.5 31.8 1.0
CG A:ASP195 3.6 34.1 1.0
N A:TYR229 3.9 28.9 1.0
N A:ASP230 4.0 30.9 1.0
CA A:ASP230 4.1 32.0 1.0
CA A:CA709 4.1 75.5 1.0
CA A:TYR229 4.1 29.3 1.0
OD2 A:ASP195 4.3 33.9 1.0
OD2 A:ASP241 4.3 33.4 1.0
O A:ASP241 4.3 37.3 1.0
CB A:ASP241 4.3 36.4 1.0
OD2 A:ASP230 4.3 31.9 1.0
CB A:ASP230 4.4 31.4 1.0
CG A:ASP241 4.5 35.7 1.0
CB A:ASN228 4.5 29.5 1.0
CB A:ASP193 4.6 32.1 1.0
C A:ASN228 4.7 29.3 1.0
CB A:ASP195 4.7 33.8 1.0
CB A:GLN191 4.7 34.8 1.0
OE1 A:GLN191 4.9 29.7 1.0

Calcium binding site 3 out of 3 in 3m8d

Go back to Calcium Binding Sites List in 3m8d
Calcium binding site 3 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca711

b:88.8
occ:1.00
NE2 A:HIS176 2.4 46.2 1.0
NE2 A:HIS174 2.6 42.7 1.0
CE1 A:HIS174 2.8 42.0 1.0
CE1 A:HIS176 3.3 46.6 1.0
CD2 A:HIS176 3.4 44.7 1.0
CD2 A:HIS174 3.9 41.0 1.0
ND1 A:HIS174 4.1 41.9 1.0
ND1 A:HIS176 4.5 45.2 1.0
CG A:HIS176 4.5 41.5 1.0
CG A:HIS174 4.6 39.0 1.0

Reference:

D.M.Freed, P.S.Horanyi, M.C.Wiener, D.S.Cafiso. Conformational Exchange in A Membrane Transport Protein Is Altered in Protein Crystals. Biophys.J. V. 99 1604 2010.
ISSN: ISSN 0006-3495
PubMed: 20816073
DOI: 10.1016/J.BPJ.2010.06.026
Page generated: Sat Dec 12 04:20:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy