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Calcium in PDB 2p5v: Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis

Protein crystallography data

The structure of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis, PDB code: 2p5v was solved by J.Ren, S.Sainsbury, R.J.Owens, Oxford Protein Production Facility (Oppf), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.070, 148.480, 77.720, 90.00, 106.41, 90.00
R / Rfree (%) 17.6 / 23.8

Other elements in 2p5v:

The structure of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis (pdb code 2p5v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis, PDB code: 2p5v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2p5v

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Calcium binding site 1 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:69.0
occ:1.00
 O A:GLU105 2.3 47.1 1.0
OD1 A:ASP107 2.5 54.2 1.0
OD2 G:ASP136 2.6 82.8 1.0
OD1 G:ASP136 3.1 73.5 1.0
CG G:ASP136 3.2 68.2 1.0
C A:GLU105 3.3 44.6 1.0
O A:HOH1058 3.3 50.8 1.0
CG A:ASP107 3.5 52.0 1.0
CA A:GLU105 3.9 48.6 1.0
OD2 A:ASP107 4.0 58.4 1.0
O A:HOH405 4.1 62.8 1.0
N A:ASP107 4.2 46.9 1.0
N A:THR106 4.4 47.3 1.0
O A:GLY104 4.5 43.4 1.0
CB G:ASP136 4.5 51.4 1.0
C A:THR106 4.6 48.0 1.0
CA A:THR106 4.7 51.2 1.0
CB A:GLU105 4.7 47.0 1.0
CB A:ASP107 4.7 48.6 1.0
O G:ALA137 4.7 39.4 1.0
CA A:ASP107 4.8 41.1 1.0
OG A:SER75 4.9 64.6 1.0

Calcium binding site 2 out of 8 in 2p5v

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Calcium binding site 2 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


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 Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1008

b:63.0
occ:1.00
 O B:GLU105 2.4 41.3 1.0
O D:HOH421 2.4 42.0 1.0
OD2 D:ASP136 2.4 78.2 1.0
OD1 B:ASP107 2.5 53.4 1.0
O B:HOH539 3.0 49.0 1.0
CG D:ASP136 3.3 69.5 1.0
C B:GLU105 3.4 49.4 1.0
OD1 D:ASP136 3.4 82.0 1.0
O B:HOH533 3.5 53.0 1.0
CG B:ASP107 3.6 57.0 1.0
CA B:GLU105 4.0 51.4 1.0
OD2 B:ASP107 4.0 54.7 1.0
N B:ASP107 4.3 49.4 1.0
N B:THR106 4.4 48.3 1.0
O D:HOH1038 4.5 51.2 1.0
O B:GLY104 4.5 49.4 1.0
C B:THR106 4.6 49.2 1.0
CB D:ASP136 4.7 53.9 1.0
CA B:THR106 4.7 50.6 1.0
O B:HOH1081 4.8 61.1 1.0
CB B:GLU105 4.8 55.1 1.0
O D:ALA137 4.8 45.4 1.0
CB B:ASP107 4.8 45.0 1.0
CA B:ASP107 4.9 47.3 1.0

Calcium binding site 3 out of 8 in 2p5v

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Calcium binding site 3 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


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 Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:59.6
occ:1.00
 O C:GLU105 2.3 50.3 1.0
OD2 A:ASP136 2.3 78.4 1.0
OD1 C:ASP107 2.5 45.7 1.0
O A:HOH285 2.7 46.1 1.0
O C:HOH1126 3.0 56.5 1.0
C C:GLU105 3.3 41.2 1.0
CG A:ASP136 3.3 71.0 1.0
CG C:ASP107 3.4 51.6 1.0
OD1 A:ASP136 3.7 63.5 1.0
O C:HOH1104 3.8 49.1 1.0
OD2 C:ASP107 3.8 52.3 1.0
CA C:GLU105 3.9 47.0 1.0
O C:HOH365 4.0 57.6 1.0
N C:ASP107 4.2 46.7 1.0
N C:THR106 4.4 40.9 1.0
O C:GLY104 4.5 44.3 1.0
NZ C:LYS78 4.5 60.5 1.0
C C:THR106 4.6 45.3 1.0
CB A:ASP136 4.6 58.6 1.0
CB C:ASP107 4.6 44.8 1.0
O A:HOH409 4.7 53.1 1.0
CB C:GLU105 4.7 49.0 1.0
CA C:THR106 4.7 44.1 1.0
CA C:ASP107 4.7 47.5 1.0
OG C:SER75 4.9 61.0 1.0
O A:ALA137 5.0 46.0 1.0

Calcium binding site 4 out of 8 in 2p5v

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Calcium binding site 4 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1002

b:48.8
occ:1.00
 O E:HOH293 2.3 53.0 1.0
O C:HOH1161 2.4 62.1 1.0
OD2 C:ASP136 2.4 47.6 1.0
O E:GLU105 2.4 41.4 1.0
OD1 E:ASP107 2.6 43.7 1.0
CG C:ASP136 3.2 49.4 1.0
OD1 C:ASP136 3.3 50.6 1.0
C E:GLU105 3.4 42.1 1.0
CG E:ASP107 3.5 37.1 1.0
OD2 E:ASP107 3.9 49.1 1.0
CA E:GLU105 4.0 51.1 1.0
O E:HOH338 4.1 36.5 1.0
N E:ASP107 4.4 40.9 1.0
O E:GLY104 4.4 47.2 1.0
O C:HOH1067 4.5 48.5 1.0
CB C:ASP136 4.5 42.1 1.0
N E:THR106 4.5 46.5 1.0
NZ E:LYS78 4.5 59.6 1.0
O C:ALA137 4.7 45.1 1.0
O E:HOH328 4.7 88.8 1.0
C E:THR106 4.7 48.4 1.0
CB E:ASP107 4.7 41.9 1.0
CA E:ASP107 4.8 46.9 1.0
CB E:GLU105 4.8 52.1 1.0
CA E:THR106 4.9 46.1 1.0

Calcium binding site 5 out of 8 in 2p5v

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Calcium binding site 5 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


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 Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1007

b:53.4
occ:1.00
 O F:HOH442 2.4 48.7 1.0
O D:GLU105 2.4 44.6 1.0
OD1 D:ASP107 2.6 49.6 1.0
O D:HOH1047 2.7 50.9 1.0
OD2 F:ASP136 2.7 80.8 1.0
O F:HOH251 2.8 40.6 1.0
OD1 F:ASP136 3.2 86.3 1.0
CG F:ASP136 3.3 72.3 1.0
CG D:ASP107 3.4 53.8 1.0
C D:GLU105 3.5 44.2 1.0
OD2 D:ASP107 3.7 54.0 1.0
O D:HOH367 4.2 47.7 1.0
N D:ASP107 4.2 44.0 1.0
CA D:GLU105 4.2 48.8 1.0
N D:THR106 4.5 48.1 1.0
NZ D:LYS78 4.6 74.0 1.0
CB D:ASP107 4.6 52.2 1.0
C D:THR106 4.6 54.0 1.0
O F:HOH318 4.6 42.5 1.0
CA D:ASP107 4.7 48.7 1.0
O D:GLY104 4.7 42.9 1.0
CG D:GLU105 4.7 66.2 1.0
CA D:THR106 4.7 53.1 1.0
CB F:ASP136 4.8 53.2 1.0
O F:ALA137 4.9 44.4 1.0
OG D:SER75 5.0 54.9 1.0

Calcium binding site 6 out of 8 in 2p5v

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Calcium binding site 6 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1005

b:64.1
occ:1.00
 O F:GLU105 2.4 42.1 1.0
OD1 F:ASP107 2.4 49.4 1.0
OD1 H:ASP136 2.5 76.1 1.0
O F:HOH1300 2.6 62.3 1.0
O F:HOH1099 2.8 53.1 1.0
O F:HOH993 2.9 51.4 1.0
O F:HOH376 3.1 42.4 1.0
CG H:ASP136 3.3 65.4 1.0
CG F:ASP107 3.4 51.1 1.0
C F:GLU105 3.4 46.2 1.0
OD2 H:ASP136 3.5 63.0 1.0
OD2 F:ASP107 3.7 54.0 1.0
CA F:GLU105 4.0 53.1 1.0
N F:ASP107 4.2 49.4 1.0
N F:THR106 4.4 51.1 1.0
C F:THR106 4.6 52.2 1.0
CB F:ASP107 4.6 47.8 1.0
CB H:ASP136 4.6 51.4 1.0
CB F:GLU105 4.6 55.8 1.0
O F:GLY104 4.7 46.4 1.0
CA F:THR106 4.7 49.4 1.0
CA F:ASP107 4.7 48.0 1.0
OG F:SER75 4.9 49.1 1.0

Calcium binding site 7 out of 8 in 2p5v

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Calcium binding site 7 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1003

b:57.7
occ:1.00
 O G:GLU105 2.2 46.5 1.0
OD1 G:ASP107 2.4 54.1 1.0
OD2 E:ASP136 2.4 60.0 1.0
CG E:ASP136 3.2 50.0 1.0
C G:GLU105 3.3 46.9 1.0
OD1 E:ASP136 3.4 55.0 1.0
CG G:ASP107 3.4 49.3 1.0
O G:HOH380 3.5 48.2 1.0
OD2 G:ASP107 3.9 48.4 1.0
CA G:GLU105 3.9 47.7 1.0
N G:ASP107 4.2 45.8 1.0
O G:HOH473 4.2 76.5 1.0
N G:THR106 4.4 44.9 1.0
CB E:ASP136 4.5 45.4 1.0
O G:GLY104 4.6 45.4 1.0
C G:THR106 4.6 48.3 1.0
CB G:ASP107 4.7 48.6 1.0
CB G:GLU105 4.7 49.7 1.0
O E:HOH356 4.7 50.7 1.0
CA G:ASP107 4.7 46.0 1.0
CA G:THR106 4.7 47.0 1.0
O E:ALA137 4.8 46.2 1.0

Calcium binding site 8 out of 8 in 2p5v

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Calcium binding site 8 out of 8 in the Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Transcriptional Regulator NMB0573 From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1006

b:58.0
occ:1.00
 OD2 B:ASP136 2.2 67.0 1.0
O H:HOH545 2.3 58.1 1.0
O B:HOH209 2.3 44.5 1.0
O H:GLU105 2.4 51.4 1.0
OD1 H:ASP107 2.5 48.2 1.0
O H:HOH1307 2.9 56.6 1.0
CG B:ASP136 3.2 60.3 1.0
C H:GLU105 3.4 45.9 1.0
CG H:ASP107 3.5 53.2 1.0
OD1 B:ASP136 3.5 61.7 1.0
OD2 H:ASP107 3.9 55.0 1.0
CA H:GLU105 3.9 51.7 1.0
N H:ASP107 4.3 46.9 1.0
O H:GLY104 4.4 43.9 1.0
N H:THR106 4.4 47.1 1.0
CG H:GLU105 4.5 63.2 1.0
CB B:ASP136 4.5 50.7 1.0
O B:HOH544 4.6 44.7 1.0
C H:THR106 4.6 48.0 1.0
CB H:ASP107 4.7 46.0 1.0
CA H:ASP107 4.7 47.3 1.0
CA H:THR106 4.7 46.2 1.0
O B:ALA137 4.8 46.8 1.0
CB H:GLU105 4.8 49.0 1.0

Reference:

J.Ren, S.Sainsbury, S.E.Combs, R.G.Capper, P.W.Jordan, N.S.Berrow, D.K.Stammers, N.J.Saunders, R.J.Owens. The Structure and Transcriptional Analysis of A Global Regulator From Neisseria Meningitidis. J.Biol.Chem. V. 282 14655 2007.
ISSN: ISSN 0021-9258
PubMed: 17374605
DOI: 10.1074/JBC.M701082200
Page generated: Fri Jul 12 15:00:04 2024

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