Magnesium in PDB 6okv: PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation

Protein crystallography data

The structure of PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation, PDB code: 6okv was solved by M.Mccallum, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 4.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.510, 127.130, 187.260, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation (pdb code 6okv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation, PDB code: 6okv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6okv

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Magnesium binding site 1 out of 4 in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:53.5
occ:1.00
O2G A:ANP402 1.9 54.7 1.0
O2B A:ANP402 2.0 53.1 1.0
OG A:SER138 2.1 62.1 1.0
PG A:ANP402 3.1 55.2 1.0
CB A:SER138 3.2 62.5 1.0
PB A:ANP402 3.2 53.5 1.0
OE2 A:GLU164 3.5 66.8 1.0
N3B A:ANP402 3.5 54.6 0.7
OE1 A:GLU164 3.6 67.1 1.0
O3G A:ANP402 3.9 55.3 0.9
CD A:GLU164 4.0 67.0 1.0
O1B A:ANP402 4.0 53.4 0.9
N A:SER138 4.0 66.1 1.0
O1A A:ANP402 4.1 53.0 0.9
CA A:SER138 4.1 65.2 1.0
O1G A:ANP402 4.2 56.0 0.8
O3A A:ANP402 4.5 53.2 0.9
PA A:ANP402 4.9 52.7 1.0

Magnesium binding site 2 out of 4 in 6okv

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Magnesium binding site 2 out of 4 in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:60.9
occ:1.00
O2G B:ANP402 1.9 61.2 1.0
O2B B:ANP402 1.9 61.6 1.0
OG B:SER138 2.0 81.5 1.0
PG B:ANP402 3.1 61.9 1.0
PB B:ANP402 3.2 62.2 1.0
CB B:SER138 3.2 81.5 1.0
OE2 B:GLU164 3.3 88.5 1.0
OE1 B:GLU164 3.4 87.7 1.0
N3B B:ANP402 3.4 62.4 0.7
CD B:GLU164 3.7 88.3 1.0
O1A B:ANP402 3.9 62.1 0.9
O3G B:ANP402 3.9 61.8 0.9
O1B B:ANP402 4.0 62.2 0.9
N B:SER138 4.1 81.0 1.0
O1G B:ANP402 4.2 62.1 0.8
CA B:SER138 4.2 80.6 1.0
O3A B:ANP402 4.4 62.7 0.9
PA B:ANP402 4.7 62.6 1.0

Magnesium binding site 3 out of 4 in 6okv

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Magnesium binding site 3 out of 4 in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:96.9
occ:1.00
O2G D:ANP402 2.0 98.2 1.0
O2B D:ANP402 2.0 96.7 1.0
OG D:SER138 2.1 63.2 1.0
CB D:SER138 3.1 63.5 1.0
PG D:ANP402 3.2 98.8 1.0
OE2 D:GLU164 3.2 74.2 1.0
OE1 D:GLU164 3.2 77.1 1.0
PB D:ANP402 3.3 97.3 1.0
N3B D:ANP402 3.6 98.3 0.7
CD D:GLU164 3.6 75.0 1.0
O1A D:ANP402 3.9 96.3 0.9
O3G D:ANP402 4.0 99.2 0.9
N D:SER138 4.1 61.4 1.0
O1B D:ANP402 4.1 97.2 0.9
CA D:SER138 4.1 62.3 1.0
O1G D:ANP402 4.3 99.6 0.8
O3A D:ANP402 4.5 96.9 0.9
PA D:ANP402 4.8 96.3 1.0
NH2 D:ARG83 4.8 81.0 1.0

Magnesium binding site 4 out of 4 in 6okv

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Magnesium binding site 4 out of 4 in the PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PILT4 From Geobacter Metallireducens Bound to Amp-Pnp: C2CCOCCO Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:60.2
occ:1.00
O2G E:ANP402 1.9 60.3 1.0
O2B E:ANP402 1.9 60.7 1.0
OG E:SER138 2.0 64.1 1.0
PG E:ANP402 3.1 60.7 1.0
PB E:ANP402 3.2 61.1 1.0
CB E:SER138 3.2 66.6 1.0
OE1 E:GLU164 3.4 63.7 1.0
OE2 E:GLU164 3.4 60.0 1.0
N3B E:ANP402 3.4 61.1 0.7
CD E:GLU164 3.8 62.1 1.0
O3G E:ANP402 3.9 60.9 0.9
O1A E:ANP402 4.0 60.8 0.9
O1B E:ANP402 4.0 61.4 0.9
N E:SER138 4.0 63.0 1.0
CA E:SER138 4.1 64.1 1.0
O1G E:ANP402 4.2 60.6 0.8
O3A E:ANP402 4.4 61.4 0.9
PA E:ANP402 4.8 61.2 1.0
NZ E:LYS137 5.0 61.7 1.0

Reference:

M.Mccallum, S.Benlekbir, S.Nguyen, S.Tammam, J.L.Rubinstein, L.L.Burrows, P.L.Howell. Multiple Conformations Facilitate Pilt Function in the Type IV Pilus. Nat Commun V. 10 5198 2019.
ISSN: ESSN 2041-1723
PubMed: 31729381
DOI: 10.1038/S41467-019-13070-Z
Page generated: Mon Dec 14 23:43:41 2020

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