Atomistry » Calcium » PDB 3fyi-3ghg » 3gbh
Atomistry »
  Calcium »
    PDB 3fyi-3ghg »
      3gbh »

Calcium in PDB 3gbh: Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution, PDB code: 3gbh was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.51 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.850, 86.150, 160.900, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution (pdb code 3gbh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution, PDB code: 3gbh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3gbh

Go back to Calcium Binding Sites List in 3gbh
Calcium binding site 1 out of 5 in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution


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 Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca217

b:20.3
occ:1.00
O B:HOH357 2.3 31.1 1.0
OD1 B:ASP113 2.5 21.6 1.0
CG B:ASP113 3.5 22.8 1.0
OD2 B:ASP113 3.8 27.6 1.0
O B:HOH344 4.5 30.2 1.0
CB B:THR111 4.7 20.9 1.0
N B:ASP113 4.7 20.7 1.0
N B:GLU112 4.8 18.4 1.0
CB B:ASP113 4.8 23.4 1.0
CB B:GLU112 4.8 18.8 1.0

Calcium binding site 2 out of 5 in 3gbh

Go back to Calcium Binding Sites List in 3gbh
Calcium binding site 2 out of 5 in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution


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 Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca218

b:28.2
occ:1.00
O B:HOH565 2.2 27.0 1.0
OD1 B:ASP103 2.3 28.7 1.0
OE1 B:GLU106 2.4 27.8 1.0
O C:HOH373 2.5 21.1 1.0
OE2 B:GLU106 2.5 21.8 1.0
CD B:GLU106 2.8 23.5 1.0
O B:HOH575 2.9 40.0 1.0
CG B:ASP103 3.6 29.3 1.0
O B:HOH333 4.3 25.2 1.0
O C:HOH231 4.3 25.0 1.0
CG B:GLU106 4.3 23.0 1.0
OD2 B:ASP103 4.3 29.8 1.0
N B:ASP103 4.4 24.1 1.0
CA B:ASP103 4.4 24.4 1.0
O B:GLN99 4.5 24.7 1.0
CB B:ASP103 4.6 25.5 1.0
C B:GLY102 4.7 22.9 1.0
O B:GLY102 5.0 22.4 1.0

Calcium binding site 3 out of 5 in 3gbh

Go back to Calcium Binding Sites List in 3gbh
Calcium binding site 3 out of 5 in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution


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 A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca216

b:16.6
occ:1.00
OD1 D:ASP113 2.4 20.9 1.0
O C:HOH358 2.4 20.6 1.0
CG D:ASP113 3.4 23.4 1.0
OD2 D:ASP113 3.7 25.0 1.0
CB D:THR111 4.6 21.2 1.0
N D:ASP113 4.6 21.4 1.0
N D:GLU112 4.7 19.9 1.0
CB D:ASP113 4.8 21.6 1.0
CB D:GLU112 4.8 18.9 1.0
CG2 D:THR111 5.0 21.6 1.0

Calcium binding site 4 out of 5 in 3gbh

Go back to Calcium Binding Sites List in 3gbh
Calcium binding site 4 out of 5 in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution


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 A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca217

b:20.6
occ:1.00
O C:HOH396 2.3 15.7 1.0
OD1 D:ASP103 2.3 22.7 1.0
OE1 D:GLU106 2.4 23.9 1.0
O C:HOH268 2.4 23.3 1.0
O C:HOH437 2.4 14.9 1.0
OE2 D:GLU106 2.6 22.4 1.0
CD D:GLU106 2.8 26.1 1.0
CG D:ASP103 3.6 28.0 1.0
O C:HOH374 4.3 23.2 1.0
O C:HOH354 4.3 16.7 1.0
CA D:ASP103 4.3 22.6 1.0
CG D:GLU106 4.3 22.8 1.0
OD2 D:ASP103 4.3 27.4 1.0
N D:ASP103 4.3 21.1 1.0
O D:GLN99 4.5 23.9 1.0
CB D:ASP103 4.6 22.5 1.0
C D:GLY102 4.6 20.6 1.0
O D:GLY102 4.8 20.6 1.0

Calcium binding site 5 out of 5 in 3gbh

Go back to Calcium Binding Sites List in 3gbh
Calcium binding site 5 out of 5 in the Crystal Structure of A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution


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 A Putative Nad(P)H:Fmn Oxidoreductase (SE1966) From Staphylococcus Epidermidis Atcc 12228 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca218

b:51.7
occ:1.00
OD2 D:ASP180 2.5 43.1 1.0
OD2 D:ASP178 2.7 44.3 1.0
OD1 D:ASP178 2.8 39.5 1.0
CG D:ASP178 3.1 37.2 1.0
CG D:ASP180 3.5 39.1 1.0
CB D:ASP180 3.9 32.6 1.0
CB D:ASP178 4.5 29.5 1.0
OD1 D:ASP180 4.6 44.4 1.0
N D:ASP180 4.8 31.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Jul 8 12:40:26 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy