Atomistry » Calcium » PDB 2vk5-2vuz » 2vs7
Atomistry »
  Calcium »
    PDB 2vk5-2vuz »
      2vs7 »

Calcium in PDB 2vs7: The Crystal Structure of I-Dmoi in Complex with Dna and Ca

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Dna and Ca, PDB code: 2vs7 was solved by M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.76 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.988, 70.587, 106.848, 90.00, 119.75, 90.00
R / Rfree (%) 18.7 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca (pdb code 2vs7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca, PDB code: 2vs7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2vs7

Go back to Calcium Binding Sites List in 2vs7
Calcium binding site 1 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1183

b:35.0
occ:1.00
OP1 B:DA14 2.2 37.5 1.0
O A:ALA116 2.3 31.3 1.0
OP2 C:DC16 2.4 33.8 1.0
O B:HOH2029 2.4 44.4 1.0
O A:HOH2022 2.4 33.7 1.0
OD2 A:ASP21 2.4 33.9 1.0
OD1 A:ASP21 2.6 31.7 1.0
CG A:ASP21 2.8 32.2 1.0
C A:ALA116 3.4 31.7 1.0
O B:HOH2031 3.6 24.4 1.0
P C:DC16 3.6 34.7 1.0
P B:DA14 3.7 39.1 1.0
CA A:ALA116 3.9 31.6 1.0
O C:HOH2035 4.0 45.3 1.0
O5' C:DC16 4.1 34.8 1.0
NE2 A:GLN42 4.3 45.6 1.0
CB A:ASP21 4.4 31.5 1.0
O A:HOH2076 4.4 54.0 1.0
C5' B:DA14 4.4 37.7 1.0
O3' B:DA13 4.4 41.3 1.0
C4' B:DA14 4.4 36.9 1.0
O A:VAL115 4.4 32.7 1.0
OP1 C:DC16 4.5 36.5 1.0
N A:GLU117 4.5 31.6 1.0
OE1 A:GLN42 4.5 46.1 1.0
O5' B:DA14 4.6 38.3 1.0
OP2 B:DA14 4.6 36.3 1.0
C5' C:DC16 4.6 34.1 1.0
CB A:ALA116 4.7 31.1 1.0
O3' C:DC15 4.8 35.1 1.0
CD A:GLN42 4.8 45.7 1.0
OE1 A:GLU117 4.8 35.7 1.0
CA A:GLU117 4.9 31.8 1.0
O3' B:DA14 5.0 34.5 1.0
N A:ALA116 5.0 31.4 1.0

Calcium binding site 2 out of 3 in 2vs7

Go back to Calcium Binding Sites List in 2vs7
Calcium binding site 2 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1196

b:34.1
occ:1.00
OP1 E:DA14 2.2 32.6 1.0
OD2 D:ASP21 2.3 23.9 1.0
OP2 F:DC16 2.3 34.5 1.0
O D:ALA116 2.4 29.3 1.0
O D:HOH2085 2.4 29.7 1.0
O D:HOH2089 2.5 37.5 1.0
OD1 D:ASP21 2.7 26.1 1.0
CG D:ASP21 2.8 27.8 1.0
C D:ALA116 3.4 30.0 1.0
P F:DC16 3.6 34.8 1.0
P E:DA14 3.7 34.4 1.0
O D:HOH2006 3.7 23.1 1.0
OE1 D:GLN42 3.8 36.0 1.0
CA D:ALA116 3.8 29.9 1.0
O5' F:DC16 4.2 34.0 1.0
O D:VAL115 4.3 30.6 1.0
C5' E:DA14 4.3 31.8 1.0
CB D:ASP21 4.3 27.4 1.0
NZ D:LYS120 4.3 42.6 1.0
O D:HOH2007 4.4 50.9 1.0
OP1 F:DC16 4.4 35.1 1.0
C4' E:DA14 4.4 33.0 1.0
O3' E:DA13 4.4 35.7 1.0
O5' E:DA14 4.5 32.9 1.0
OP2 E:DA14 4.6 34.9 1.0
C5' F:DC16 4.6 36.6 1.0
N D:GLU117 4.6 31.2 1.0
CD D:GLN42 4.7 35.2 1.0
NE2 D:GLN42 4.7 34.2 1.0
CB D:ALA116 4.7 29.8 1.0
O3' F:DC15 4.7 34.4 1.0
OE1 D:GLU117 4.8 41.8 1.0
N D:ALA116 5.0 30.0 1.0

Calcium binding site 3 out of 3 in 2vs7

Go back to Calcium Binding Sites List in 2vs7
Calcium binding site 3 out of 3 in the The Crystal Structure of I-Dmoi in Complex with Dna and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of I-Dmoi in Complex with Dna and Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1182

b:35.7
occ:1.00
OP1 H:DA14 2.2 36.7 1.0
OP2 I:DC16 2.3 34.4 1.0
O G:ALA116 2.3 32.6 1.0
O I:HOH2020 2.4 37.2 1.0
O G:HOH2020 2.5 36.5 1.0
OD2 G:ASP21 2.5 32.4 1.0
OD1 G:ASP21 2.7 30.9 1.0
CG G:ASP21 2.9 31.6 1.0
C G:ALA116 3.4 33.0 1.0
O G:HOH2004 3.6 26.3 1.0
P I:DC16 3.6 34.1 1.0
P H:DA14 3.7 37.0 1.0
CA G:ALA116 3.9 32.9 1.0
O I:HOH2022 3.9 45.9 1.0
O5' I:DC16 4.2 35.1 1.0
OE1 G:GLN42 4.3 48.1 1.0
C5' H:DA14 4.3 35.9 1.0
O3' H:DA13 4.3 39.9 1.0
OP1 I:DC16 4.4 37.3 1.0
C4' H:DA14 4.4 35.9 1.0
NE2 G:GLN42 4.4 46.2 1.0
CB G:ASP21 4.5 30.8 1.0
O G:VAL115 4.5 34.0 1.0
O5' H:DA14 4.5 37.9 1.0
O G:HOH2062 4.5 57.1 1.0
N G:GLU117 4.6 32.6 1.0
OP2 H:DA14 4.6 37.5 1.0
CD G:GLN42 4.6 45.7 1.0
CB G:ALA116 4.6 32.7 1.0
C5' I:DC16 4.7 34.0 1.0
O3' I:DC15 4.8 35.8 1.0
OE2 G:GLU117 4.9 39.3 1.0
CA G:GLU117 5.0 33.5 1.0

Reference:

M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya. Crystal Structure of I-Dmoi in Complex with Its Target Dna Provides New Insights Into Meganuclease Engineering. Proc.Nat.Acad.Sci.Usa V. 105 16888 2008.
ISSN: ISSN 0027-8424
PubMed: 18974222
DOI: 10.1073/PNAS.0804795105
Page generated: Sat Dec 12 03:54:22 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