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Sodium in PDB 6zt3: N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp

Enzymatic activity of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp

All present enzymatic activity of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp:
5.99.1.3;

Protein crystallography data

The structure of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp, PDB code: 6zt3 was solved by L.Feng, J.E.A.Mundy, C.E.M.Stevenson, L.A.Mitchenall, D.M.Lawson, K.Mi, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.69 / 1.56
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.985, 76.985, 261.476, 90, 90, 120
R / Rfree (%) 14.7 / 19.4

Other elements in 6zt3:

The structure of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp also contains other interesting chemical elements:

Potassium (K) 2 atoms
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp (pdb code 6zt3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp, PDB code: 6zt3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6zt3

Go back to Sodium Binding Sites List in 6zt3
Sodium binding site 1 out of 3 in the N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:20.8
occ:1.00
 O A:HOH717 2.3 18.7 1.0
O A:HOH640 2.4 26.1 1.0
O A:HOH648 2.5 24.3 1.0
O A:ASP110 2.5 21.5 1.0
O A:HOH855 2.6 27.6 1.0
O A:LYS108 2.6 18.1 1.0
C A:LYS108 3.4 17.1 1.0
C A:ASP110 3.4 21.6 1.0
CA A:LYS108 3.9 16.2 1.0
N A:ASP110 3.9 21.2 1.0
CA A:ASP110 4.1 23.2 1.0
O A:TYR114 4.1 20.1 1.0
O A:HOH802 4.2 19.0 1.0
N A:PHE109 4.3 16.0 1.0
CB A:LYS108 4.3 15.7 1.0
O A:ALA363 4.3 23.5 1.0
C A:PHE109 4.3 19.0 1.0
N A:GLY111 4.3 24.0 1.0
O A:HOH664 4.3 32.6 1.0
OG A:SER117 4.4 18.0 1.0
O A:HOH660 4.5 19.0 1.0
OE1 A:GLU364 4.5 29.3 1.0
CA A:GLY111 4.6 24.2 1.0
CA A:PHE109 4.6 17.3 1.0
O A:PHE109 4.9 22.0 1.0

Sodium binding site 2 out of 3 in 6zt3

Go back to Sodium Binding Sites List in 6zt3
Sodium binding site 2 out of 3 in the N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:22.8
occ:1.00
 O A:ASP80 2.3 18.6 1.0
OG1 A:THR167 2.3 23.7 1.0
O A:HOH836 2.3 36.5 1.0
O A:GLY81 2.3 17.9 1.0
O A:HOH847 2.4 31.0 1.0
O A:THR167 2.6 21.9 1.0
C A:ASP80 3.0 17.3 1.0
C A:GLY81 3.2 17.9 1.0
C A:THR167 3.2 20.7 1.0
CB A:THR167 3.3 24.8 1.0
O A:HOH782 3.6 40.4 1.0
N A:GLY81 3.6 17.3 1.0
CA A:THR167 3.6 22.4 1.0
CA A:GLY81 3.7 17.0 1.0
N A:THR167 3.9 24.1 1.0
CA A:ASP80 4.0 17.0 1.0
O A:HOH663 4.1 30.6 1.0
N A:GLY168 4.1 21.0 1.0
N A:ARG82 4.3 16.8 1.0
O A:HOH842 4.3 36.3 1.0
CB A:ASP80 4.4 19.0 1.0
O A:PHE61 4.5 23.9 1.0
CA A:GLY168 4.6 17.8 1.0
CG2 A:THR167 4.7 27.6 1.0
CA A:ARG82 4.7 16.3 1.0
O A:HOH609 4.7 26.3 0.5

Sodium binding site 3 out of 3 in 6zt3

Go back to Sodium Binding Sites List in 6zt3
Sodium binding site 3 out of 3 in the N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of N-Terminal 47 kDa Fragment of the Mycobacterium Smegmatis Dna Gyrase B Subunit Complexed with Adpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:45.1
occ:0.50
 O A:HOH825 2.3 39.0 1.0
O A:LYS5 2.4 42.6 1.0
OD1 A:ASN7 2.4 43.1 1.0
CG A:ASN7 3.5 42.4 1.0
C A:LYS5 3.6 43.6 1.0
N A:LYS5 3.9 38.4 1.0
N A:ASN7 4.2 40.5 1.0
ND2 A:ASN7 4.2 46.2 1.0
CA A:LYS5 4.2 40.1 1.0
CB A:ASN7 4.6 41.3 1.0
N A:ASN6 4.6 44.9 1.0
CB A:LYS5 4.6 42.5 1.0
CA A:ASN7 4.8 39.1 1.0
CA A:ASN6 4.9 39.6 1.0
C A:GLN4 4.9 41.7 1.0

Reference:

L.Feng, J.E.A.Mundy, C.E.M.Stevenson, L.A.Mitchenall, D.M.Lawson, K.Mi, A.Maxwell. The Pentapeptide-Repeat Protein, Mfpa, Interacts with Mycobacterial Dna Gyrase As A Dna T-Segment Mimic To Be Published.
Page generated: Tue Oct 8 15:40:00 2024

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