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Magnesium in PDB 4xco: Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle

Protein crystallography data

The structure of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle, PDB code: 4xco was solved by T.Hainzl, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 2.90
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.227, 112.971, 121.204, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.8

Other elements in 4xco:

The structure of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle (pdb code 4xco). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle, PDB code: 4xco:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 4xco

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Magnesium binding site 1 out of 14 in the Signal-Sequence Induced Conformational Changes in the 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 Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg301

b:83.7
occ:1.00
 O M:HOH407 1.7 71.6 1.0
O M:HOH405 1.7 84.8 1.0
O M:HOH406 1.8 71.4 1.0
OP1 M:A156 2.1 76.1 1.0
O3' M:C155 3.1 85.8 1.0
P M:A156 3.2 77.5 1.0
OP1 M:G200 3.8 89.1 1.0
H5' M:A156 4.1 0.9 1.0
OP2 M:A156 4.2 67.4 1.0
H5'' M:A156 4.2 0.9 1.0
HH11 A:ARG15 4.2 0.8 1.0
NH1 A:ARG15 4.3 94.8 1.0
HD2 A:ARG15 4.3 0.5 1.0
H5'' M:C155 4.3 0.8 1.0
O5' M:A156 4.3 82.0 1.0
OP2 M:G200 4.3 74.3 1.0
OP2 M:G217 4.3 61.9 1.0
C5' M:A156 4.4 91.5 1.0
HH12 A:ARG15 4.4 0.8 1.0
C3' M:C155 4.5 91.4 1.0
P M:G200 4.5 77.6 1.0
H4' M:C155 4.6 0.4 1.0
CZ A:ARG15 4.6 90.3 1.0
OP1 M:G217 4.7 62.7 1.0
HO2' M:C155 4.8 98.3 1.0
OP1 M:C199 4.9 98.4 1.0
C4' M:C155 4.9 89.5 1.0
NE A:ARG15 4.9 96.0 1.0
H3' M:C155 4.9 0.7 1.0
CD A:ARG15 5.0 96.2 1.0

Magnesium binding site 2 out of 14 in 4xco

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Magnesium binding site 2 out of 14 in the Signal-Sequence Induced Conformational Changes in the 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 Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg302

b:83.5
occ:1.00
 O M:HOH412 1.7 69.8 1.0
O M:HOH413 1.7 77.0 1.0
O M:HOH408 1.8 79.8 1.0
O M:HOH410 1.8 77.5 1.0
O M:HOH411 2.0 68.0 1.0
O M:HOH409 2.0 76.8 1.0
H41 M:C199 3.5 95.3 1.0
O6 M:G200 3.8 76.4 1.0
N4 M:C199 4.0 79.4 1.0
H42 M:C201 4.0 95.0 1.0
H5 M:C199 4.0 85.3 1.0
OP2 M:A219 4.1 56.2 1.0
H41 M:C201 4.2 95.0 1.0
OP2 M:C218 4.3 71.0 1.0
N4 M:C201 4.3 79.2 1.0
H42 M:C199 4.4 95.3 1.0
OP1 M:C196 4.4 85.5 1.0
OP1 M:C218 4.4 56.2 1.0
C5 M:C199 4.5 71.1 1.0
N7 M:G200 4.5 77.0 1.0
C4 M:C199 4.5 73.3 1.0
H5'' M:C196 4.6 0.5 1.0
P M:C218 4.7 0.6 1.0
C6 M:G200 4.8 72.1 1.0
O M:HOH401 4.8 75.9 1.0
H62 M:A220 4.9 0.6 1.0

Magnesium binding site 3 out of 14 in 4xco

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Magnesium binding site 3 out of 14 in the Signal-Sequence Induced Conformational Changes in the 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 Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg303

b:88.9
occ:1.00
 O M:HOH402 1.8 93.9 1.0
O M:HOH416 1.9 90.7 1.0
O M:HOH403 1.9 91.0 1.0
O M:HOH415 1.9 0.1 1.0
O6 M:G226 3.5 79.3 1.0
O6 M:G227 3.6 81.4 1.0
O M:HOH404 4.1 92.5 1.0
N7 M:G226 4.2 78.6 1.0
OP2 M:A225 4.3 87.5 1.0
C6 M:G226 4.4 72.6 1.0
C6 M:G227 4.6 79.3 1.0
C5 M:G226 4.6 65.0 1.0
H42 M:C191 4.7 90.4 1.0
H42 M:C192 4.7 97.2 1.0
N7 M:G227 4.8 75.7 1.0
H41 M:C191 5.0 90.4 1.0

Magnesium binding site 4 out of 14 in 4xco

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Magnesium binding site 4 out of 14 in the Signal-Sequence Induced Conformational Changes in the 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 Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg304

b:87.0
occ:1.00
 O M:HOH417 1.8 95.8 1.0
O M:HOH421 1.8 99.2 1.0
O M:HOH420 1.8 96.5 1.0
O M:HOH419 1.8 97.0 1.0
O M:HOH418 1.8 89.1 1.0
O M:HOH422 1.9 98.9 1.0
N7 M:G230 4.0 98.2 1.0
O6 M:G146 4.2 87.8 1.0
O6 M:G231 4.2 95.0 1.0
O6 M:G230 4.3 87.9 1.0
H61 M:A232 4.8 0.1 1.0
C5 M:G230 4.8 83.0 1.0
H62 M:A232 4.8 0.1 1.0
H62 M:A229 4.9 94.2 1.0
N7 M:G231 4.9 83.8 1.0
C6 M:G230 4.9 81.8 1.0
C8 M:G230 5.0 92.7 1.0

Magnesium binding site 5 out of 14 in 4xco

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Magnesium binding site 5 out of 14 in the Signal-Sequence Induced Conformational Changes in the 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 Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg305

b:98.2
occ:1.00
 O M:HOH433 1.8 86.6 1.0
O M:HOH434 1.8 0.6 1.0
OP2 M:G213 2.3 90.0 1.0
H8 M:G213 2.9 94.5 1.0
N7 M:G213 3.3 81.9 1.0
C8 M:G213 3.4 78.7 1.0
P M:G213 3.6 85.2 1.0
O5' M:G213 3.7 69.8 1.0
OP2 M:A212 3.8 73.5 1.0
O5' M:A212 3.8 73.0 1.0
H3' M:A212 3.8 0.8 1.0
OP1 M:A212 3.9 87.0 1.0
P M:A212 4.0 91.0 1.0
H5'' M:A212 4.1 83.0 1.0
H21 M:G209 4.5 0.3 1.0
C5' M:A212 4.5 69.2 1.0
C3' M:A212 4.6 84.8 1.0
O3' M:A212 4.6 75.7 1.0
OP1 M:G213 4.7 0.6 1.0
C5 M:G213 4.7 62.6 1.0
N9 M:G213 4.7 66.8 1.0
H8 M:A212 4.9 0.5 1.0

Magnesium binding site 6 out of 14 in 4xco

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Magnesium binding site 6 out of 14 in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg306

b:80.5
occ:1.00
 O M:HOH427 1.8 90.3 1.0
O M:HOH426 1.8 57.6 1.0
O M:HOH425 2.0 88.4 1.0
O M:HOH424 2.1 0.3 1.0
O M:HOH428 2.1 85.3 1.0
OP2 M:G209 2.3 66.8 1.0
P M:G209 3.6 65.5 1.0
HZ2 A:LYS51 3.6 0.4 1.0
HZ3 A:LYS51 3.7 0.4 1.0
H8 M:G209 3.8 87.6 1.0
O5' M:G209 4.0 64.9 1.0
NZ A:LYS51 4.0 85.3 1.0
HZ1 A:LYS51 4.1 0.4 1.0
H3' M:C208 4.1 70.2 1.0
N7 M:G209 4.1 61.9 1.0
C8 M:G209 4.2 73.0 1.0
OP2 M:C208 4.3 65.9 1.0
OP1 M:G209 4.4 78.3 1.0
O5' M:C208 4.7 56.2 1.0
H3' M:G209 4.7 83.5 1.0
O3' M:C208 4.7 56.2 1.0
OP2 M:G210 4.8 56.2 1.0
C3' M:C208 4.9 58.5 1.0
P M:C208 5.0 67.9 1.0

Magnesium binding site 7 out of 14 in 4xco

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Magnesium binding site 7 out of 14 in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg307

b:99.7
occ:1.00
 O M:HOH432 2.1 78.3 1.0
O M:HOH431 2.1 90.5 1.0
O M:HOH429 2.1 94.8 1.0
O M:HOH430 2.1 87.4 1.0
OP2 M:G204 2.2 0.1 1.0
P M:G204 3.5 88.5 1.0
OP1 M:G204 4.0 0.9 1.0
OP1 M:A203 4.1 92.2 1.0
O5' M:G204 4.1 86.7 1.0
N7 M:G205 4.3 83.7 1.0
H41 M:C206 4.3 86.2 1.0
H3' M:A203 4.5 0.4 1.0
O5' M:A203 4.5 0.9 1.0
H8 M:G204 4.6 0.3 1.0
O6 M:G205 4.6 88.0 1.0
P M:A203 4.7 94.9 1.0
O3' M:A203 4.7 92.2 1.0
H5'' M:A203 4.7 0.9 1.0
OP2 M:A203 4.8 88.2 1.0
OP2 M:G205 4.8 98.6 1.0

Magnesium binding site 8 out of 14 in 4xco

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Magnesium binding site 8 out of 14 in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:89.1
occ:1.00
 O M:HOH438 1.9 97.8 1.0
O A:GLY70 2.3 91.7 1.0
O A:LYS69 2.8 0.1 1.0
OP2 M:U164 3.1 84.4 1.0
O5' M:U164 3.3 83.9 1.0
HE1 A:MET1 3.4 0.3 1.0
C A:LYS69 3.4 97.1 1.0
C A:GLY70 3.5 98.7 1.0
O A:HOH202 3.5 92.8 1.0
P M:U164 3.8 78.2 1.0
HA A:LYS69 3.9 0.1 1.0
N A:GLY70 3.9 87.1 1.0
CE A:MET1 4.0 86.9 1.0
HE3 A:MET1 4.0 0.3 1.0
HE2 A:MET1 4.0 0.3 1.0
O4' M:U164 4.0 91.3 1.0
CA A:GLY70 4.1 94.6 1.0
HA A:ASN71 4.2 86.1 1.0
CA A:LYS69 4.2 97.6 1.0
HA2 A:GLY70 4.3 0.6 1.0
H4' M:U164 4.3 93.8 1.0
H3' M:G163 4.4 90.3 1.0
C5' M:U164 4.5 71.0 1.0
N A:ASN71 4.5 89.3 1.0
C4' M:U164 4.5 78.2 1.0
H A:GLY70 4.6 0.5 1.0
OP1 M:U164 4.7 84.4 1.0
H A:LYS69 4.7 0.4 1.0
O5' M:G163 4.8 86.7 1.0
CA A:ASN71 4.8 71.8 1.0
N A:LYS69 4.8 0.2 1.0
HD2 A:TYR68 4.8 0.5 1.0
H6 M:U164 4.9 0.2 1.0
OP2 M:G163 4.9 71.6 1.0
OP1 M:G163 4.9 89.6 1.0
H5'' M:U164 5.0 85.2 1.0
H A:LYS72 5.0 97.2 1.0

Magnesium binding site 9 out of 14 in 4xco

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Magnesium binding site 9 out of 14 in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:78.8
occ:1.00
 O E:HOH403 2.1 94.5 1.0
OP2 E:G204 2.3 76.5 1.0
P E:G204 3.6 93.4 1.0
N7 E:G205 3.7 68.6 1.0
OP1 E:A203 3.7 0.5 1.0
O6 E:G205 3.9 81.9 1.0
H8 E:G204 4.0 87.1 1.0
O5' E:G204 4.0 89.9 1.0
H41 E:C206 4.1 84.6 1.0
OP2 E:A203 4.1 87.6 1.0
O5' E:A203 4.1 85.1 1.0
P E:A203 4.1 0.0 1.0
H3' E:A203 4.2 0.9 1.0
N7 E:G204 4.3 72.0 1.0
C8 E:G204 4.4 72.6 1.0
OP1 E:G204 4.4 1.0 1.0
C5 E:G205 4.5 59.2 1.0
C6 E:G205 4.6 65.2 1.0
H21 E:G217 4.6 93.0 1.0
H61 E:A216 4.7 88.7 1.0
N4 E:C206 4.7 70.5 1.0
H5'' E:A203 4.7 0.7 1.0
O3' E:A203 4.7 73.7 1.0
C8 E:G205 4.8 65.3 1.0
H8 E:G205 4.9 78.3 1.0
C3' E:A203 4.9 85.7 1.0
H3' E:G204 5.0 97.8 1.0
C5' E:A203 5.0 88.0 1.0
H42 E:C206 5.0 84.6 1.0

Magnesium binding site 10 out of 14 in 4xco

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Magnesium binding site 10 out of 14 in the Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:75.3
occ:1.00
 O E:HOH409 2.1 89.0 1.0
O E:HOH407 2.1 67.9 1.0
O E:HOH404 2.1 79.1 1.0
O E:HOH405 2.1 62.2 1.0
O E:HOH406 2.1 74.4 1.0
O E:HOH413 2.1 71.2 1.0
H41 E:C199 3.6 96.2 1.0
H42 E:C201 3.9 91.7 1.0
OP2 E:A219 3.9 70.3 1.0
O6 E:G200 4.1 80.1 1.0
OP1 E:C218 4.1 87.1 1.0
N4 E:C199 4.1 80.2 1.0
H41 E:C201 4.2 91.7 1.0
H5 E:C199 4.2 84.3 1.0
OP2 E:C218 4.3 76.9 1.0
N4 E:C201 4.3 76.4 1.0
OP1 E:C196 4.4 90.8 1.0
H42 E:C199 4.5 96.2 1.0
P E:C218 4.6 80.3 1.0
C4 E:C199 4.6 69.1 1.0
C5 E:C199 4.6 70.2 1.0
H5'' E:C196 4.6 0.2 1.0
N7 E:G200 4.7 67.3 1.0
H62 E:A220 4.8 82.3 1.0

Reference:

T.Hainzl, A.E.Sauer-Eriksson. Signal-Sequence Induced Conformational Changes in the Signal Recognition Particle. Nat Commun V. 6 7163 2015.
ISSN: ESSN 2041-1723
PubMed: 26051119
DOI: 10.1038/NCOMMS8163
Page generated: Tue Aug 20 15:25:40 2024

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