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Magnesium in PDB 3hax: Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus

Protein crystallography data

The structure of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus, PDB code: 3hax was solved by K.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.11
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 187.809, 63.696, 83.848, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22

Other elements in 3hax:

The structure of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus also contains other interesting chemical elements:

Fluorine (F) 1 atom
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus (pdb code 3hax). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus, PDB code: 3hax:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3hax

Go back to Magnesium Binding Sites List in 3hax
Magnesium binding site 1 out of 5 in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg200

b:19.0
occ:1.00
 O E:HOH404 2.2 18.5 1.0
O E:HOH401 2.2 19.1 1.0
O E:HOH403 2.2 18.4 1.0
O E:HOH402 2.2 17.8 1.0
O E:HOH405 2.2 18.8 1.0
O E:HOH406 2.2 17.9 1.0
O E:HOH537 4.0 21.5 1.0
O6 E:G21 4.1 19.5 1.0
O E:HOH514 4.1 21.8 1.0
O E:HOH516 4.2 15.3 1.0
N7 E:G20 4.2 19.8 1.0
O E:HOH505 4.3 11.0 1.0
O6 E:G20 4.3 19.7 1.0
O E:HOH584 4.5 25.7 1.0
N7 E:G21 4.6 18.9 1.0
O6 E:G22 4.6 19.6 1.0
O E:HOH563 4.7 44.5 1.0
O E:HOH544 4.8 23.4 1.0
C5 E:G20 4.8 19.8 1.0
C6 E:G20 4.9 19.8 1.0
C6 E:G21 5.0 19.4 1.0

Magnesium binding site 2 out of 5 in 3hax

Go back to Magnesium Binding Sites List in 3hax
Magnesium binding site 2 out of 5 in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:29.4
occ:1.00
 O E:HOH411 2.2 28.9 1.0
O E:HOH413 2.2 28.8 1.0
O E:HOH412 2.2 28.6 1.0
O E:HOH414 2.2 29.1 1.0
O3' E:G53 4.0 20.6 1.0
O E:HOH577 4.2 38.3 1.0
OP1 E:A54 4.3 21.0 1.0
O2' E:G53 4.8 19.3 1.0
C4' E:G53 4.8 20.6 1.0
P E:A54 4.9 20.9 1.0
C3' E:G53 5.0 20.1 1.0

Magnesium binding site 3 out of 5 in 3hax

Go back to Magnesium Binding Sites List in 3hax
Magnesium binding site 3 out of 5 in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:23.9
occ:1.00
 OP1 E:C37 2.2 21.9 1.0
O E:HOH423 2.2 24.3 1.0
O E:HOH424 2.2 23.6 1.0
O E:HOH422 2.2 23.8 1.0
O E:HOH421 2.2 23.5 1.0
P E:C37 3.5 21.3 1.0
O5' E:C37 4.1 20.9 1.0
OP2 E:C37 4.1 21.1 1.0
C5' E:C37 4.3 19.7 1.0
OP2 E:C38 4.3 18.5 1.0
O3' E:C36 4.6 21.3 1.0

Magnesium binding site 4 out of 5 in 3hax

Go back to Magnesium Binding Sites List in 3hax
Magnesium binding site 4 out of 5 in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg203

b:30.0
occ:1.00
 O E:HOH433 2.2 29.4 1.0
O E:HOH431 2.2 29.0 1.0
O E:HOH432 2.2 28.9 1.0
O E:HOH570 4.0 25.1 1.0
O E:HOH517 4.2 24.1 1.0
O6 E:G39 4.3 16.3 1.0
N7 E:G39 4.4 16.1 1.0
O E:HOH557 4.5 26.5 1.0
O6 E:G40 4.5 18.7 1.0
O E:HOH520 4.6 20.3 1.0
N4 E:C18 4.8 21.6 1.0
N4 E:C38 4.9 18.7 1.0

Magnesium binding site 5 out of 5 in 3hax

Go back to Magnesium Binding Sites List in 3hax
Magnesium binding site 5 out of 5 in the Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Substrate-Bound GAR1-Minus H/Aca Rnp From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:34.8
occ:1.00
 O E:HOH443 2.2 34.3 1.0
O E:HOH442 2.2 34.5 1.0
O E:HOH444 2.2 33.7 1.0
O E:HOH441 2.2 34.3 1.0
O6 E:G53 4.3 18.5 1.0
O6 E:G52 4.3 23.7 1.0
N7 E:G52 4.3 23.6 1.0
N7 E:G53 4.4 18.6 1.0
N4 E:C51 4.9 27.5 1.0
C6 E:G52 5.0 23.7 1.0
C5 E:G52 5.0 23.6 1.0

Reference:

J.Duan, L.Li, J.Lu, W.Wang, K.Ye. Structural Mechanism of Substrate Rna Recruitment in H/Aca Rna-Guided Pseudouridine Synthase. Mol.Cell V. 34 427 2009.
ISSN: ISSN 1097-2765
PubMed: 19481523
DOI: 10.1016/J.MOLCEL.2009.05.005
Page generated: Wed Aug 14 15:06:48 2024

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