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Magnesium in PDB 1mfq: Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle

Protein crystallography data

The structure of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle, PDB code: 1mfq was solved by A.Kuglstatter, C.Oubridge, K.Nagai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 3.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.180, 131.180, 204.051, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 26.7

Other elements in 1mfq:

The structure of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle (pdb code 1mfq). 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 Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle, PDB code: 1mfq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1mfq

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Magnesium binding site 1 out of 5 in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:77.8
occ:1.00
OP2 A:G193 2.5 63.8 1.0
OP1 A:A192 3.1 62.9 1.0
N7 A:G194 3.5 49.7 1.0
O6 A:G194 3.7 46.6 1.0
P A:G193 3.8 64.3 1.0
O4 A:U195 3.8 40.9 1.0
P A:A192 4.0 63.3 1.0
O5' A:G193 4.1 60.5 1.0
OP2 A:A192 4.2 63.0 1.0
C5 A:G194 4.3 49.4 1.0
C6 A:G194 4.3 47.0 1.0
O5' A:A192 4.3 61.5 1.0
N7 A:G193 4.4 54.9 1.0
C8 A:G193 4.5 56.6 1.0
C8 A:G194 4.6 50.2 1.0
OP1 A:G193 4.8 65.9 1.0
C4 A:U195 4.8 37.7 1.0
O3' A:A192 4.8 61.2 1.0
C3' A:A192 5.0 60.1 1.0

Magnesium binding site 2 out of 5 in 1mfq

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Magnesium binding site 2 out of 5 in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:54.3
occ:1.00
OP1 A:C185 1.8 59.7 1.0
OP2 A:A183 2.2 72.1 1.0
P A:C185 3.3 60.1 1.0
P A:A183 3.6 66.9 1.0
O3' A:G182 4.0 68.6 1.0
O5' A:C185 4.0 55.8 1.0
OP2 A:C186 4.1 54.0 1.0
OP2 A:C185 4.1 63.1 1.0
C5' A:C185 4.2 50.4 1.0
O3' A:A184 4.2 61.7 1.0
C5' A:A183 4.5 59.9 1.0
O5' A:A183 4.5 65.0 1.0
OP1 A:A183 4.6 69.4 1.0
OP2 A:A208 4.8 54.0 1.0
C8 A:A183 4.9 80.1 1.0

Magnesium binding site 3 out of 5 in 1mfq

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Magnesium binding site 3 out of 5 in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:59.7
occ:1.00
OP2 A:A205 2.2 49.8 1.0
P A:A205 3.6 50.2 1.0
N7 A:G206 3.8 45.1 1.0
O5' A:A205 3.9 44.6 1.0
N7 A:A205 4.0 41.1 1.0
C8 A:A205 4.3 40.5 1.0
C3' A:G204 4.5 44.0 1.0
O3' A:G204 4.5 47.9 1.0
C8 A:G206 4.6 45.4 1.0
OP1 A:A205 4.6 50.1 1.0
O6 A:G206 4.7 44.5 1.0
C5 A:G206 4.8 43.2 1.0
O5' A:G204 5.0 51.6 1.0

Magnesium binding site 4 out of 5 in 1mfq

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Magnesium binding site 4 out of 5 in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:80.2
occ:1.00
OP1 A:A183 1.9 69.4 1.0
P A:A183 3.2 66.9 1.0
O5' A:A183 3.8 65.0 1.0
OP1 A:G182 3.9 72.1 1.0
O5' A:G182 3.9 70.5 1.0
OP2 A:G182 4.0 70.0 1.0
OP2 A:A183 4.0 72.1 1.0
P A:G182 4.1 72.8 1.0
O3' A:G182 4.4 68.6 1.0
C3' A:G182 4.4 67.6 1.0
C5' A:G182 4.5 68.7 1.0
O4 A:U211 5.0 66.8 1.0

Magnesium binding site 5 out of 5 in 1mfq

Go back to Magnesium Binding Sites List in 1mfq
Magnesium binding site 5 out of 5 in the Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure Analysis of A Ternary S-Domain Complex of Human Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:82.0
occ:1.00
OP2 A:U117 2.4 0.0 1.0
P A:U117 2.8 0.4 1.0
OP1 A:U117 2.9 0.8 1.0
O3' A:C116 3.1 0.5 1.0
C5' A:C116 3.5 0.5 1.0
O5' A:C116 3.6 0.2 1.0
C3' A:C116 3.6 1.0 1.0
OP1 A:C116 3.9 0.9 1.0
C4' A:C116 4.0 0.6 1.0
P A:C116 4.3 0.1 1.0
O5' A:U117 4.4 0.6 1.0
OP2 A:C116 4.8 0.3 1.0

Reference:

A.Kuglstatter, C.Oubridge, K.Nagai. Induced Structural Changes of 7SL Rna During the Assembly of Human Signal Recognition Particle Nat.Struct.Biol. V. 9 740 2002.
ISSN: ISSN 1072-8368
PubMed: 12244299
DOI: 10.1038/NSB843
Page generated: Mon Dec 14 06:28:37 2020

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