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Nickel in PDB 3kkc: The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V

Protein crystallography data

The structure of The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V, PDB code: 3kkc was solved by K.Tan, C.Hatzos, T.Morgan, S.Clancy, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.351, 128.681, 74.566, 90.00, 103.23, 90.00
R / Rfree (%) 20.8 / 27.9

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V (pdb code 3kkc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V, PDB code: 3kkc:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3kkc

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Nickel binding site 1 out of 4 in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:71.5
occ:0.80
NE2 A:HIS87 2.2 87.0 1.0
NE2 A:HIS67 2.2 65.6 1.0
NE2 A:HIS83 2.3 79.2 1.0
N1 A:IMD212 2.3 89.9 0.7
N1 A:IMD213 2.8 85.0 0.7
C2 A:IMD213 3.0 89.3 0.7
CE1 A:HIS87 3.0 82.5 1.0
N3 A:IMD211 3.0 0.1 0.7
C2 A:IMD212 3.1 90.3 0.7
CD2 A:HIS67 3.1 70.2 1.0
CD2 A:HIS83 3.1 78.8 1.0
CD2 A:HIS87 3.2 83.0 1.0
CE1 A:HIS67 3.2 71.4 1.0
C5 A:IMD212 3.3 93.3 0.7
CE1 A:HIS83 3.3 74.5 1.0
C5 A:IMD213 3.4 83.8 0.7
C4 A:IMD211 3.6 0.6 0.7
N3 A:IMD213 3.6 88.3 0.7
C2 A:IMD211 3.8 0.9 0.7
C4 A:IMD213 3.8 86.2 0.7
ND1 A:HIS87 4.2 80.9 1.0
N3 A:IMD212 4.2 90.8 0.7
CG A:HIS67 4.3 70.6 1.0
CG A:HIS83 4.3 78.2 1.0
CG A:HIS87 4.3 78.3 1.0
ND1 A:HIS67 4.3 69.6 1.0
C4 A:IMD212 4.3 93.7 0.7
ND1 A:HIS83 4.4 79.2 1.0
C5 A:IMD211 4.5 0.8 0.7
N1 A:IMD211 4.6 0.6 0.7

Nickel binding site 2 out of 4 in 3kkc

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Nickel binding site 2 out of 4 in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:75.7
occ:0.80
NE2 B:HIS83 2.4 84.1 1.0
NE2 B:HIS87 2.4 95.1 1.0
NE2 B:HIS67 2.4 85.6 1.0
N3 B:IMD213 2.5 0.6 0.7
N3 B:IMD211 2.5 87.9 0.7
C2 B:IMD212 2.7 0.0 0.7
N3 B:IMD212 2.8 0.2 0.7
CD2 B:HIS83 3.2 83.3 1.0
CE1 B:HIS67 3.2 89.5 1.0
C2 B:IMD213 3.3 0.8 0.7
C2 B:IMD211 3.3 91.6 0.7
C4 B:IMD213 3.3 0.5 0.7
CD2 B:HIS87 3.3 86.0 1.0
CE1 B:HIS87 3.4 91.0 1.0
CD2 B:HIS67 3.4 81.3 1.0
CE1 B:HIS83 3.5 87.3 1.0
C4 B:IMD211 3.7 88.4 0.7
N1 B:IMD212 4.0 0.1 0.7
C4 B:IMD212 4.1 0.6 0.7
N1 B:IMD213 4.3 0.1 0.7
C5 B:IMD213 4.3 0.3 0.7
ND1 B:HIS67 4.4 86.5 1.0
CG B:HIS83 4.4 81.6 1.0
ND1 B:HIS87 4.5 86.2 1.0
CG B:HIS87 4.5 78.7 1.0
ND1 B:HIS83 4.5 86.9 1.0
CG B:HIS67 4.5 81.3 1.0
N1 B:IMD211 4.5 94.0 0.7
C5 B:IMD212 4.7 0.3 0.7
C5 B:IMD211 4.7 91.0 0.7
NE2 B:GLN92 4.8 94.5 1.0
NH2 B:ARG73 4.8 0.6 1.0

Nickel binding site 3 out of 4 in 3kkc

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Nickel binding site 3 out of 4 in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni201

b:70.0
occ:0.80
NE2 C:HIS67 2.2 71.7 1.0
NE2 C:HIS87 2.4 87.4 1.0
N3 C:IMD213 2.5 91.0 0.7
N3 C:IMD211 2.5 0.7 0.7
NE2 C:HIS83 2.5 76.4 1.0
C4 C:IMD213 2.7 91.3 0.7
CE1 C:HIS87 2.7 87.1 1.0
C4 C:IMD212 2.8 0.8 0.7
N3 C:IMD212 2.8 0.2 0.7
C2 C:IMD211 2.9 0.8 0.7
CE1 C:HIS67 3.1 73.9 1.0
C4 C:IMD211 3.2 0.1 0.7
CD2 C:HIS67 3.2 74.1 1.0
CD2 C:HIS83 3.3 74.5 1.0
CD2 C:HIS87 3.6 81.4 1.0
CE1 C:HIS83 3.6 81.7 1.0
C2 C:IMD213 3.6 94.0 0.7
N1 C:IMD211 3.8 0.6 0.7
C5 C:IMD213 3.8 92.3 0.7
ND1 C:HIS87 3.9 81.8 1.0
C5 C:IMD211 3.9 0.7 0.7
C2 C:IMD212 4.2 0.0 0.7
C5 C:IMD212 4.2 0.9 0.7
ND1 C:HIS67 4.3 74.9 1.0
N1 C:IMD213 4.3 94.0 0.7
CG C:HIS87 4.3 77.9 1.0
CG C:HIS67 4.3 77.4 1.0
NH2 C:ARG73 4.4 0.4 1.0
OE1 C:GLN92 4.5 89.9 1.0
CG C:HIS83 4.6 80.1 1.0
ND1 C:HIS83 4.7 85.5 1.0
N1 C:IMD212 4.8 0.1 0.7

Nickel binding site 4 out of 4 in 3kkc

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Nickel binding site 4 out of 4 in the The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni201

b:87.9
occ:0.80
NE2 D:HIS87 2.3 0.8 1.0
NE2 D:HIS67 2.3 0.0 1.0
NE2 D:HIS83 2.5 0.9 1.0
N1 D:IMD212 2.5 0.8 0.7
N3 D:IMD213 2.8 0.3 0.7
CE1 D:HIS67 3.0 0.0 1.0
C2 D:IMD212 3.1 0.9 0.7
CD2 D:HIS87 3.2 0.8 1.0
C5 D:IMD211 3.2 88.0 0.7
N1 D:IMD211 3.2 86.4 0.7
CE1 D:HIS83 3.2 0.6 1.0
C2 D:IMD213 3.3 0.7 0.7
CE1 D:HIS87 3.4 0.8 1.0
CD2 D:HIS67 3.4 0.0 1.0
CD2 D:HIS83 3.5 0.6 1.0
C5 D:IMD212 3.7 0.8 0.7
C2 D:IMD211 4.0 86.3 0.7
C4 D:IMD211 4.0 89.2 0.7
C4 D:IMD213 4.1 0.8 0.7
ND1 D:HIS67 4.1 0.6 1.0
NH2 D:ARG73 4.2 0.5 1.0
N3 D:IMD212 4.3 0.8 0.7
CG D:HIS67 4.4 0.2 1.0
CG D:HIS87 4.4 0.7 1.0
ND1 D:HIS83 4.4 1.0 1.0
ND1 D:HIS87 4.4 98.7 1.0
N3 D:IMD211 4.5 87.1 0.7
CG D:HIS83 4.5 0.8 1.0
C4 D:IMD212 4.6 0.0 0.7
N1 D:IMD213 4.6 0.8 0.7
NE2 D:GLN92 4.9 0.9 1.0
C5 D:IMD213 5.0 0.9 0.7

Reference:

K.Tan, C.Hatzos, T.Morgan, S.Clancy, A.Joachimiak. The Crystal Structure of Tetr Transcriptional Regulator From Streptococcus Agalactiae 2603V To Be Published.
Page generated: Fri Sep 25 08:26:23 2020
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