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Sodium in PDB 3m7k: Crystal Structure of Paci-Dna Enzyme Product Complex

Protein crystallography data

The structure of Crystal Structure of Paci-Dna Enzyme Product Complex, PDB code: 3m7k was solved by B.W.Shen, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.26 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 37.089, 114.927, 114.322, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 3m7k:

The structure of Crystal Structure of Paci-Dna Enzyme Product Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 2 atoms
Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Paci-Dna Enzyme Product Complex (pdb code 3m7k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Paci-Dna Enzyme Product Complex, PDB code: 3m7k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3m7k

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Sodium binding site 1 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na147

b:51.6
occ:1.00
 O A:HOH244 2.3 33.0 1.0
O A:HIS77 3.2 36.8 1.0
O B:HOH68 3.8 49.2 1.0
NH2 A:ARG78 3.9 39.6 1.0
CA A:ARG78 4.1 34.6 1.0
N A:THR79 4.2 33.5 1.0
C A:HIS77 4.3 36.8 1.0
CZ A:ARG78 4.3 39.4 1.0
OG1 A:THR79 4.4 36.1 1.0
C A:ARG78 4.5 34.3 1.0
CG2 A:THR79 4.5 35.4 1.0
N A:ARG78 4.6 34.5 1.0
NE A:ARG78 4.8 37.8 1.0
CD A:ARG78 4.8 37.2 1.0
NH1 A:ARG78 4.9 39.0 1.0
CB A:THR79 4.9 34.5 1.0

Sodium binding site 2 out of 9 in 3m7k

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Sodium binding site 2 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na148

b:51.2
occ:1.00
 O A:HOH219 2.5 64.0 1.0
O1 A:SO4156 2.6 50.1 0.5
O A:HOH213 3.1 52.9 1.0
O A:GLN60 3.1 42.5 1.0
N A:HIS62 3.2 37.7 1.0
O A:HIS62 3.5 37.0 1.0
O2 A:SO4156 3.6 50.6 0.5
S A:SO4156 3.6 50.2 0.5
O4 A:SO4155 3.7 47.9 0.5
CD2 A:LEU107 3.8 39.5 1.0
CA A:ARG61 3.8 38.9 1.0
C A:ARG61 4.0 38.6 1.0
O1 A:SO4155 4.1 48.1 0.5
CA A:HIS62 4.1 37.4 1.0
C A:GLN60 4.1 41.8 1.0
CB A:HIS62 4.2 37.7 1.0
C A:HIS62 4.3 37.0 1.0
O4 A:SO4156 4.4 49.8 0.5
ND1 A:HIS62 4.4 43.9 1.0
N A:ARG61 4.5 40.6 1.0
S A:SO4155 4.5 47.9 0.5
O A:HOH238 4.7 60.7 1.0
O3 A:SO4156 4.8 49.5 0.5
CG A:HIS62 4.8 40.8 1.0
CB A:ARG61 4.9 38.6 1.0

Sodium binding site 3 out of 9 in 3m7k

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Sodium binding site 3 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na149

b:64.9
occ:1.00
 O A:HOH211 2.4 59.4 1.0
O A:ASN44 4.1 49.3 1.0
O A:PHE46 4.5 44.7 1.0
CG2 A:THR47 4.8 43.0 1.0
O A:THR45 4.9 47.3 1.0
CA A:THR45 5.0 47.8 1.0

Sodium binding site 4 out of 9 in 3m7k

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Sodium binding site 4 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na150

b:65.1
occ:1.00
 O A:HOH225 2.4 43.2 1.0
CB A:ALA12 2.9 52.8 1.0
O A:HOH198 3.1 58.8 1.0
O A:HOH205 3.6 48.2 1.0
OD1 A:ASP14 3.8 50.9 1.0
N A:ALA12 3.9 53.5 1.0
CA A:ALA12 4.0 52.9 1.0
CD1 A:LEU57 4.5 39.5 1.0
CG A:ASP14 4.7 49.7 1.0
OD2 A:ASP14 4.8 49.3 1.0

Sodium binding site 5 out of 9 in 3m7k

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Sodium binding site 5 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na151

b:63.1
occ:1.00
 O A:HOH246 2.0 59.8 1.0
O A:HOH237 2.1 59.0 1.0
O A:HOH245 2.8 68.7 1.0
CB A:HIS85 3.4 39.7 1.0
CG A:HIS85 3.7 41.6 1.0
ND1 A:HIS77 4.0 44.5 1.0
CB A:HIS77 4.1 38.9 1.0
CA A:HIS85 4.1 38.6 1.0
CD2 A:HIS85 4.2 41.2 1.0
ND1 A:HIS85 4.2 44.5 1.0
CG A:HIS77 4.5 42.3 1.0
O A:HIS77 4.5 36.8 1.0
N A:HIS85 4.6 39.1 1.0
CA A:HIS77 4.6 37.9 1.0
CG2 A:THR79 4.8 35.4 1.0
C A:HIS77 4.8 36.8 1.0
CE1 A:HIS85 4.9 44.3 1.0
NE2 A:HIS85 5.0 41.7 1.0

Sodium binding site 6 out of 9 in 3m7k

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Sodium binding site 6 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na152

b:51.3
occ:1.00
 O A:HOH231 2.3 49.4 1.0
O A:HOH221 2.6 47.9 1.0
O A:LYS134 4.0 42.7 1.0
CA A:ALA135 4.1 43.1 1.0
O A:HOH234 4.4 48.1 1.0
CA A:GLY138 4.4 49.0 1.0
C A:LYS134 4.5 43.4 1.0
N A:ALA135 4.5 43.0 1.0
O A:HOH173 4.5 40.0 1.0
O A:ALA135 4.6 43.6 1.0
C A:ALA135 4.8 43.9 1.0
CB A:ALA135 4.9 42.8 1.0

Sodium binding site 7 out of 9 in 3m7k

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Sodium binding site 7 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na153

b:53.4
occ:1.00
 O A:HOH202 2.7 0.2 1.0
O A:VAL127 2.9 38.9 1.0
OE1 A:GLU130 3.2 48.9 0.5
CG1 A:VAL127 3.5 42.4 1.0
CB A:GLU130 3.7 43.0 0.5
OE1 A:GLU130 3.8 48.5 0.5
CB A:GLU130 3.8 42.9 0.5
C A:VAL127 3.9 38.9 1.0
N A:ALA131 4.1 41.2 1.0
CD A:GLU130 4.2 48.1 0.5
CA A:VAL127 4.3 40.3 1.0
CD A:GLU130 4.3 47.7 0.5
CG A:GLU130 4.4 44.5 0.5
CG A:GLU130 4.5 45.1 0.5
CB A:ALA131 4.5 39.4 1.0
CB A:VAL127 4.5 40.6 1.0
C A:GLU130 4.6 41.9 1.0
CA A:GLU130 4.7 42.1 0.5
CA A:ALA131 4.7 39.7 1.0
CA A:GLU130 4.7 42.0 0.5
N A:LEU128 5.0 37.7 0.5
N A:LEU128 5.0 38.4 0.5

Sodium binding site 8 out of 9 in 3m7k

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Sodium binding site 8 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na11

b:57.6
occ:1.00
 O A:HOH171 2.4 41.5 1.0
O B:HOH83 3.3 64.1 1.0
O B:HOH21 3.7 34.1 1.0
O B:HOH44 3.9 38.4 1.0
O B:HOH117 4.4 45.6 1.0
O A:HOH210 4.4 55.9 1.0

Sodium binding site 9 out of 9 in 3m7k

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Sodium binding site 9 out of 9 in the Crystal Structure of Paci-Dna Enzyme Product Complex


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 Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na6

b:54.4
occ:1.00
 O C:HOH36 2.1 32.2 1.0
O A:HOH162 2.2 39.4 1.0
O C:HOH5 3.0 31.3 1.0
OP2 C:DA12 3.4 21.0 1.0
N A:LEU33 3.8 38.5 1.0
CA A:LEU33 3.9 39.7 1.0
O A:THR29 3.9 34.8 1.0
CG2 A:THR29 4.0 33.6 1.0
CB A:LEU33 4.0 39.8 1.0
CB A:ASN32 4.1 36.8 1.0
ND2 A:ASN36 4.2 33.7 1.0
C A:ASN32 4.3 38.0 1.0
OH A:TYR100 4.4 39.3 1.0
C3' C:DT11 4.4 21.9 1.0
N A:VAL91 4.6 28.6 1.0
CG2 A:VAL91 4.7 32.8 1.0
CG A:LEU33 4.7 40.9 1.0
CB A:VAL91 4.7 30.0 1.0
O A:ASN32 4.8 37.7 1.0
P C:DA12 4.8 21.4 1.0
CA A:ASN32 4.8 37.6 1.0
C A:THR29 4.8 35.7 1.0
C5' C:DT11 4.9 25.5 1.0
CD1 A:LEU33 4.9 41.6 1.0
CZ A:TYR100 5.0 40.2 1.0

Reference:

B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, B.L.Stoddard. Unusual Target Site Disruption By the Rare-Cutting Hnh Restriction Endonuclease Paci. Structure V. 18 734 2010.
ISSN: ISSN 0969-2126
PubMed: 20541511
DOI: 10.1016/J.STR.2010.03.009
Page generated: Mon Oct 7 11:26:12 2024

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