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Sodium in PDB 2z3b: Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus, PDB code: 2z3b was solved by S.H.Rho, H.H.Park, G.B.Kang, Y.J.Lim, M.S.Kang, B.K.Lim, I.S.Seong, C.H.Chung, J.Wang, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.050, 106.800, 152.700, 90.00, 112.00, 90.00
R / Rfree (%) 22.6 / 26.5

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus (pdb code 2z3b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus, PDB code: 2z3b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 2z3b

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Sodium binding site 1 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:49.9
occ:1.00
 O A:GLY164 2.7 44.7 1.0
O A:THR170 3.0 41.0 1.0
O A:CYS167 3.2 39.7 1.0
C A:GLY164 3.9 45.5 1.0
C A:CYS167 4.1 38.2 1.0
CA A:VAL168 4.2 38.4 1.0
C A:THR170 4.2 41.8 1.0
N A:VAL168 4.5 37.5 1.0
C A:VAL168 4.6 37.8 1.0
O A:VAL168 4.6 38.6 1.0
CA A:GLY164 4.7 44.3 1.0
N A:GLU165 4.9 47.0 1.0
CA A:ASN171 4.9 46.5 1.0
O A:GLU165 4.9 48.4 1.0
C A:GLU165 5.0 47.5 1.0
CA A:GLU165 5.0 49.0 1.0

Sodium binding site 2 out of 12 in 2z3b

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Sodium binding site 2 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:44.7
occ:1.00
 O B:HOH1010 2.4 39.7 1.0
O B:GLY164 2.7 34.0 1.0
O B:THR170 3.1 32.6 1.0
O B:CYS167 3.3 30.8 1.0
C B:GLY164 3.8 33.8 1.0
C B:CYS167 4.2 30.0 1.0
C B:THR170 4.3 32.0 1.0
CA B:VAL168 4.4 32.0 1.0
O B:VAL168 4.6 33.2 1.0
CA B:GLY164 4.6 33.2 1.0
C B:VAL168 4.6 32.2 1.0
N B:VAL168 4.7 30.6 1.0
CA B:ASN171 4.8 34.3 1.0
N B:GLU165 4.8 34.5 1.0
N B:ASN171 5.0 33.3 1.0
OE1 B:GLN24 5.0 34.0 1.0

Sodium binding site 3 out of 12 in 2z3b

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Sodium binding site 3 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1003

b:43.5
occ:1.00
 O C:HOH1024 2.3 33.1 1.0
O C:GLY164 2.6 34.0 1.0
O C:THR170 3.0 33.8 1.0
O C:CYS167 3.2 33.0 1.0
C C:GLY164 3.8 36.2 1.0
C C:CYS167 4.1 33.1 1.0
C C:THR170 4.2 32.6 1.0
CA C:VAL168 4.3 32.7 1.0
O C:VAL168 4.5 30.7 1.0
CA C:GLY164 4.5 34.6 1.0
C C:VAL168 4.6 31.2 1.0
N C:VAL168 4.6 32.5 1.0
CA C:ASN171 4.8 34.1 1.0
N C:GLU165 4.8 38.2 1.0
OE1 C:GLN24 4.9 30.5 1.0
N C:ASN171 5.0 33.0 1.0

Sodium binding site 4 out of 12 in 2z3b

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Sodium binding site 4 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1004

b:58.3
occ:1.00
 O D:GLY164 2.7 42.1 1.0
O D:THR170 3.0 39.3 1.0
O D:CYS167 3.2 38.6 1.0
C D:GLY164 3.9 41.8 1.0
C D:CYS167 4.1 38.3 1.0
C D:THR170 4.1 39.4 1.0
CA D:VAL168 4.2 38.6 1.0
C D:VAL168 4.5 37.8 1.0
N D:VAL168 4.6 38.0 1.0
O D:VAL168 4.6 39.1 1.0
CA D:ASN171 4.6 42.4 1.0
CA D:GLY164 4.7 39.7 1.0
OE1 D:GLN24 4.9 40.4 1.0
N D:THR170 4.9 38.6 1.0
N D:ASN171 4.9 40.1 1.0
N D:GLU165 5.0 43.6 1.0

Sodium binding site 5 out of 12 in 2z3b

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Sodium binding site 5 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1005

b:47.0
occ:1.00
 O E:GLY164 2.6 33.8 1.0
O E:THR170 2.8 30.1 1.0
O E:CYS167 3.2 30.6 1.0
C E:GLY164 3.8 33.1 1.0
C E:THR170 4.0 29.9 1.0
C E:CYS167 4.2 29.1 1.0
CA E:VAL168 4.3 30.2 1.0
C E:VAL168 4.5 30.0 1.0
CA E:GLY164 4.6 31.3 1.0
O E:VAL168 4.6 30.7 1.0
CA E:ASN171 4.6 32.1 1.0
N E:VAL168 4.7 28.5 1.0
N E:ASN171 4.8 29.9 1.0
N E:GLU165 4.9 34.4 1.0
N E:THR170 4.9 29.5 1.0
OE1 E:GLN24 5.0 31.7 1.0

Sodium binding site 6 out of 12 in 2z3b

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Sodium binding site 6 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1006

b:45.0
occ:1.00
 O F:GLY164 2.6 35.7 1.0
O F:THR170 2.9 33.1 1.0
O F:CYS167 3.3 30.1 1.0
C F:GLY164 3.8 36.2 1.0
C F:THR170 4.1 32.6 1.0
C F:CYS167 4.2 30.4 1.0
CA F:VAL168 4.3 29.9 1.0
CA F:GLY164 4.5 34.7 1.0
CA F:ASN171 4.6 34.5 1.0
N F:VAL168 4.6 30.3 1.0
C F:VAL168 4.6 29.3 1.0
O F:VAL168 4.6 29.6 1.0
N F:ASN171 4.8 32.9 1.0
N F:GLU165 4.9 37.7 1.0
N F:THR170 4.9 31.2 1.0
OE1 F:GLN24 5.0 32.0 1.0

Sodium binding site 7 out of 12 in 2z3b

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Sodium binding site 7 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1007

b:87.4
occ:1.00
 O G:GLY164 2.5 83.3 1.0
O G:CYS167 3.1 78.3 1.0
O G:THR170 3.6 77.2 1.0
C G:GLY164 3.7 82.0 1.0
C G:CYS167 4.0 77.4 1.0
O G:GLU165 4.1 88.4 1.0
CA G:VAL168 4.2 79.6 1.0
C G:GLU165 4.3 85.7 1.0
CA G:GLU165 4.4 86.2 1.0
N G:VAL168 4.5 78.1 1.0
N G:GLU165 4.5 83.0 1.0
CA G:GLY164 4.7 79.0 1.0
N G:CYS167 4.7 77.7 1.0
N G:ILE166 4.8 83.0 1.0
C G:THR170 4.8 76.0 1.0
C G:VAL168 4.9 77.8 1.0
C G:ILE166 5.0 80.5 1.0

Sodium binding site 8 out of 12 in 2z3b

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Sodium binding site 8 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1010

b:83.0
occ:1.00
 O H:GLY164 2.7 74.7 1.0
O H:CYS167 3.3 72.8 1.0
C H:GLY164 3.8 74.0 1.0
O H:THR170 3.9 69.1 1.0
O H:GLU165 4.1 81.5 1.0
C H:CYS167 4.1 72.4 1.0
C H:GLU165 4.2 79.5 1.0
CA H:VAL168 4.3 73.8 1.0
CA H:GLU165 4.4 79.1 1.0
CG2 J:VAL32 4.4 81.0 1.0
N H:GLU165 4.5 76.0 1.0
N H:VAL168 4.6 72.9 1.0
N H:ILE166 4.7 77.9 1.0
C H:ILE166 4.9 76.8 1.0
OE1 J:GLN24 4.9 73.5 1.0
N H:CYS167 4.9 73.7 1.0
CA H:GLY164 5.0 71.6 1.0

Sodium binding site 9 out of 12 in 2z3b

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Sodium binding site 9 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1009

b:83.1
occ:1.00
 O I:GLY164 2.5 85.7 1.0
O I:THR170 2.7 81.2 1.0
O I:CYS167 2.9 80.9 1.0
C I:GLY164 3.6 86.7 1.0
C I:CYS167 3.8 79.8 1.0
C I:THR170 3.8 80.4 1.0
CA I:VAL168 4.0 80.0 1.0
C I:VAL168 4.3 78.0 1.0
N I:VAL168 4.3 79.4 1.0
CA I:GLY164 4.4 84.9 1.0
O I:VAL168 4.4 78.6 1.0
N I:THR170 4.5 76.7 1.0
OE1 I:GLN24 4.5 78.5 1.0
CA I:THR170 4.7 77.7 1.0
N I:ASN171 4.7 81.2 1.0
N I:GLU165 4.7 89.0 1.0
N I:CYS167 4.7 82.5 1.0
CA I:ASN171 4.8 84.2 1.0
CA I:CYS167 4.9 80.0 1.0

Sodium binding site 10 out of 12 in 2z3b

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Sodium binding site 10 out of 12 in the Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Bacillus Subtilis Codw, A Non-Canonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na1008

b:79.8
occ:1.00
 O J:GLY164 2.7 71.3 1.0
O J:THR170 2.7 70.6 1.0
O J:CYS167 3.0 70.9 1.0
C J:GLY164 3.8 71.4 1.0
C J:THR170 3.9 70.7 1.0
C J:CYS167 4.1 70.0 1.0
CA J:VAL168 4.1 71.2 1.0
CA J:GLY164 4.5 70.4 1.0
C J:VAL168 4.5 71.1 1.0
CA J:ASN171 4.6 73.5 1.0
N J:VAL168 4.6 70.3 1.0
OE1 J:GLN24 4.6 73.5 1.0
O J:VAL168 4.7 72.5 1.0
N J:ASN171 4.7 71.7 1.0
N J:THR170 4.8 69.4 1.0
N J:GLU165 4.9 72.5 1.0
CA J:THR170 4.9 69.6 1.0

Reference:

S.H.Rho, H.H.Park, G.B.Kang, Y.J.Im, M.S.Kang, B.K.Lim, I.S.Seong, J.Seol, C.H.Chung, J.Wang, S.H.Eom. Crystal Structure of Bacillus Subtilis Codw, A Noncanonical Hslv-Like Peptidase with An Impaired Catalytic Apparatus Proteins V. 71 1020 2007.
ISSN: ISSN 0887-3585
PubMed: 17979190
DOI: 10.1002/PROT.21758
Page generated: Mon Oct 7 05:30:06 2024

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