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Manganese in PDB 7nwl: Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp

Manganese Binding Sites:

The binding sites of Manganese atom in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp (pdb code 7nwl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp, PDB code: 7nwl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7nwl

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Manganese binding site 1 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1101

b:71.8
occ:1.00
 OD2 A:ASP247 1.8 52.8 1.0
OG A:SER241 2.0 58.8 1.0
O A:THR245 2.0 71.3 1.0
CG A:ASP247 2.6 52.8 1.0
OD1 A:ASP243 2.7 72.8 1.0
OE2 A:GLU239 2.7 63.8 1.0
OD1 A:ASP247 2.8 52.8 1.0
C A:THR245 3.0 71.3 1.0
OE1 A:GLU239 3.1 63.8 1.0
CD A:GLU239 3.2 63.8 1.0
CB A:SER241 3.2 58.8 1.0
CA A:THR245 3.7 71.3 1.0
N A:THR245 3.7 71.3 1.0
CG A:ASP243 3.7 72.8 1.0
CB A:THR245 3.8 71.3 1.0
N A:SER241 3.9 58.8 1.0
CA A:SER241 4.0 58.8 1.0
C A:GLU246 4.0 63.3 1.0
CB A:ASP247 4.1 52.8 1.0
N A:GLU246 4.1 63.3 1.0
O A:GLU246 4.1 63.3 1.0
OD2 A:ASP243 4.2 72.8 1.0
N A:ASP247 4.2 52.8 1.0
N A:GLY242 4.5 70.7 1.0
CG A:GLU239 4.5 63.8 1.0
CA A:GLU246 4.5 63.3 1.0
CA A:ASP247 4.6 52.8 1.0
CA A:GLU239 4.6 63.8 1.0
CG2 A:THR245 4.6 71.3 1.0
N A:PHE240 4.6 59.1 1.0
N A:ASP243 4.7 72.8 1.0
C A:SER241 4.7 58.8 1.0
OD1 A:ASN266 4.7 67.2 1.0
OG1 A:THR245 4.8 71.3 1.0
CB A:GLU239 4.8 63.8 1.0
N A:ASP244 4.9 69.9 1.0
C A:ASP244 4.9 69.9 1.0
CB A:ASP243 5.0 72.8 1.0

Manganese binding site 2 out of 7 in 7nwl

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Manganese binding site 2 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1102

b:69.4
occ:1.00
 OD1 A:ASN295 2.1 55.5 1.0
OD1 A:ASP297 2.2 61.7 1.0
OD2 A:ASP297 2.5 61.7 1.0
CG A:ASP297 2.6 61.7 1.0
OD1 A:ASP293 2.7 56.8 1.0
OD1 A:ASP301 2.8 57.8 1.0
O A:LEU299 2.8 60.7 1.0
OD2 A:ASP301 2.9 57.8 1.0
CG A:ASN295 3.1 55.5 1.0
CG A:ASP301 3.2 57.8 1.0
ND2 A:ASN295 3.4 55.5 1.0
CG A:ASP293 3.9 56.8 1.0
C A:LEU299 3.9 60.7 1.0
CB A:ASP297 4.1 61.7 1.0
N A:ASN295 4.4 55.5 1.0
CB A:LEU299 4.4 60.7 1.0
N A:ASP297 4.4 61.7 1.0
CB A:ASN295 4.4 55.5 1.0
CA A:LEU299 4.5 60.7 1.0
N A:LEU299 4.5 60.7 1.0
CA A:ASP293 4.6 56.8 1.0
O A:GLN329 4.6 61.8 1.0
CB A:ASP293 4.6 56.8 1.0
N A:VAL294 4.6 51.4 1.0
CB A:ASP301 4.7 57.8 1.0
CD2 A:LEU328 4.7 58.9 1.0
O A:ASP300 4.8 67.6 1.0
C A:ASP300 4.8 67.6 1.0
OD2 A:ASP293 4.8 56.8 1.0
CA A:ASP297 4.8 61.7 1.0
CA A:ASN295 4.8 55.5 1.0
N A:GLN329 4.8 61.8 1.0
N A:ASP300 4.9 67.6 1.0
N A:GLY296 5.0 59.7 1.0

Manganese binding site 3 out of 7 in 7nwl

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Manganese binding site 3 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1103

b:64.8
occ:1.00
 O A:TYR366 2.0 56.7 1.0
OD1 A:ASP364 2.3 64.5 1.0
OD1 A:ASP362 2.5 64.0 1.0
OD1 A:ASP368 2.5 51.4 1.0
CG A:ASP364 2.9 64.5 1.0
OD2 A:ASP364 2.9 64.5 1.0
OD2 A:ASP368 2.9 51.4 1.0
OD1 A:ASP360 3.0 58.1 1.0
CG A:ASP368 3.0 51.4 1.0
C A:TYR366 3.2 56.7 1.0
CG A:ASP362 3.4 64.0 1.0
OD2 A:ASP362 3.7 64.0 1.0
CG A:ASP360 3.8 58.1 1.0
N A:GLY389 3.9 58.5 1.0
CA A:TYR366 4.0 56.7 1.0
C A:ASN367 4.1 51.5 1.0
O A:ASN367 4.1 51.5 1.0
N A:TYR366 4.1 56.7 1.0
CB A:TYR366 4.2 56.7 1.0
N A:ASN367 4.2 51.5 1.0
CA A:GLY389 4.3 58.5 1.0
CB A:ASP364 4.3 64.5 1.0
CA A:ASN367 4.4 51.5 1.0
OD2 A:ASP360 4.4 58.1 1.0
CB A:ASP368 4.4 51.4 1.0
N A:ASP368 4.4 51.4 1.0
N A:ASP362 4.5 64.0 1.0
N A:ASP364 4.5 64.5 1.0
CA A:ASP360 4.6 58.1 1.0
O A:GLY389 4.6 58.5 1.0
N A:LEU361 4.6 51.0 1.0
CB A:ASP360 4.7 58.1 1.0
CB A:ASP362 4.8 64.0 1.0
CA A:ASP364 4.9 64.5 1.0
CA A:ASP368 4.9 51.4 1.0
N A:GLN363 5.0 67.8 1.0
C A:ASP360 5.0 58.1 1.0
C A:GLY389 5.0 58.5 1.0

Manganese binding site 4 out of 7 in 7nwl

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Manganese binding site 4 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1104

b:70.3
occ:1.00
 O A:TYR430 1.8 65.4 1.0
OD1 A:ASN428 1.9 67.6 1.0
OD1 A:ASP426 2.0 64.4 1.0
OD1 A:ASP432 2.7 47.7 1.0
CG A:ASN428 2.9 67.6 1.0
OD1 A:ASP424 2.9 59.0 1.0
CG A:ASP426 3.0 64.4 1.0
C A:TYR430 3.0 65.4 1.0
ND2 A:ASN428 3.3 67.6 1.0
CG A:ASP432 3.3 47.7 1.0
OD2 A:ASP432 3.3 47.7 1.0
OD2 A:ASP426 3.4 64.4 1.0
CG A:ASP424 3.6 59.0 1.0
CA A:TYR430 3.9 65.4 1.0
N A:TYR430 3.9 65.4 1.0
N A:PRO431 4.0 49.1 1.0
N A:ASP426 4.1 64.4 1.0
N A:ASN428 4.2 67.6 1.0
C A:PRO431 4.2 49.1 1.0
CB A:ASN428 4.2 67.6 1.0
OD2 A:ASP424 4.2 59.0 1.0
CA A:PRO431 4.2 49.1 1.0
CB A:TYR430 4.2 65.4 1.0
CB A:ASP426 4.3 64.4 1.0
N A:ASP432 4.4 47.7 1.0
CB A:ASP424 4.5 59.0 1.0
CA A:ASP424 4.5 59.0 1.0
N A:GLY427 4.5 63.9 1.0
N A:LEU425 4.5 59.2 1.0
O A:PRO431 4.6 49.1 1.0
CA A:ASP426 4.6 64.4 1.0
CA A:ASN428 4.6 67.6 1.0
CB A:ASP432 4.7 47.7 1.0
O A:GLY448 4.7 62.2 1.0
C A:ASP424 4.8 59.0 1.0
C A:ASP426 4.8 64.4 1.0
N A:GLY448 4.8 62.2 1.0
N A:GLY429 4.8 66.7 1.0
C A:ASN428 4.9 67.6 1.0

Manganese binding site 5 out of 7 in 7nwl

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Manganese binding site 5 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:59.3
occ:1.00
 OE1 B:GLU229 2.0 49.5 1.0
OG B:SER134 2.2 52.8 1.0
OG B:SER132 2.3 52.4 1.0
OD1 C:ASP1495 2.5 55.6 1.0
CB B:SER132 3.0 52.4 1.0
CD B:GLU229 3.2 49.5 1.0
CB B:SER134 3.5 52.8 1.0
CG C:ASP1495 3.7 55.6 1.0
OD1 B:ASP259 3.7 54.9 1.0
CG B:GLU229 3.8 49.5 1.0
CB B:ALA260 3.8 47.5 1.0
OE2 B:GLU229 4.2 49.5 1.0
OD2 B:ASP130 4.3 47.3 1.0
O B:SER227 4.3 56.2 1.0
CA B:SER132 4.3 52.4 1.0
N B:SER134 4.3 52.8 1.0
CA B:SER134 4.4 52.8 1.0
CA C:ASP1495 4.5 55.6 1.0
O C:ASP1495 4.5 55.6 1.0
CB C:ASP1495 4.6 55.6 1.0
OD2 C:ASP1495 4.6 55.6 1.0
ND2 B:ASN224 4.7 51.9 1.0
C B:SER132 4.7 52.4 1.0
CG B:ASP259 4.7 54.9 1.0
N B:TYR133 4.8 58.4 1.0
C B:SER134 4.9 52.8 1.0
N B:MET135 4.9 51.9 1.0
CG B:MET135 5.0 51.9 1.0
OD2 B:ASP259 5.0 54.9 1.0

Manganese binding site 6 out of 7 in 7nwl

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Manganese binding site 6 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn802

b:67.0
occ:1.00
 OD2 B:ASP259 2.3 54.9 1.0
O B:SER134 2.4 52.8 1.0
OD2 B:ASP138 2.7 56.9 1.0
OD1 B:ASP137 2.8 60.2 1.0
OD2 B:ASP137 3.3 60.2 1.0
CG B:ASP137 3.4 60.2 1.0
C B:SER134 3.5 52.8 1.0
CG B:ASP259 3.5 54.9 1.0
CG B:ASP138 3.6 56.9 1.0
OH C:TYR1446 3.8 67.7 1.0
CA B:MET135 4.0 51.9 1.0
OD1 B:ASP138 4.2 56.9 1.0
CB B:ASP259 4.2 54.9 1.0
N B:MET135 4.2 51.9 1.0
OD1 B:ASP259 4.5 54.9 1.0
CA B:SER134 4.6 52.8 1.0
CB B:ASP138 4.6 56.9 1.0
CB B:SER134 4.7 52.8 1.0
N B:ASP138 4.8 56.9 1.0
C B:MET135 4.8 51.9 1.0
OG B:SER134 4.9 52.8 1.0
CB B:ASP137 4.9 60.2 1.0
CG B:MET135 4.9 51.9 1.0

Manganese binding site 7 out of 7 in 7nwl

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Manganese binding site 7 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 (Open Form) in Complex with Fibronectin and TS2/16 Fv-Clasp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn803

b:63.4
occ:1.00
 OD1 B:ASN224 1.8 51.9 1.0
OD1 B:ASP226 2.0 57.8 1.0
O B:PRO228 2.1 51.5 1.0
OE2 B:GLU229 2.5 49.5 1.0
OE1 B:GLU169 2.9 49.0 1.0
CG B:ASN224 3.0 51.9 1.0
O B:ASP226 3.1 57.8 1.0
C B:PRO228 3.1 51.5 1.0
CG B:ASP226 3.2 57.8 1.0
CD B:GLU229 3.4 49.5 1.0
CA B:GLU229 3.6 49.5 1.0
ND2 B:ASN224 3.6 51.9 1.0
N B:GLU229 3.7 49.5 1.0
CD B:GLU169 3.7 49.0 1.0
C B:ASP226 3.8 57.8 1.0
OD2 B:ASP226 3.9 57.8 1.0
CG B:GLU169 4.1 49.0 1.0
CB B:ASN224 4.2 51.9 1.0
OE1 B:GLU229 4.2 49.5 1.0
CG B:GLU229 4.2 49.5 1.0
CB B:ASP226 4.2 57.8 1.0
CA B:ASP226 4.3 57.8 1.0
C B:SER227 4.3 56.2 1.0
CB B:GLU229 4.3 49.5 1.0
N B:PRO228 4.3 51.5 1.0
CA B:PRO228 4.3 51.5 1.0
O B:SER227 4.3 56.2 1.0
N B:ASP226 4.4 57.8 1.0
CB B:GLU169 4.6 49.0 1.0
N B:SER227 4.6 56.2 1.0
C B:GLU229 4.7 49.5 1.0
OE2 B:GLU169 4.7 49.0 1.0
CE1 B:HIS263 4.8 44.7 1.0
O B:VAL168 5.0 41.1 1.0
CA B:SER227 5.0 56.2 1.0
N B:GLY230 5.0 46.1 1.0

Reference:

S.Schumacher, D.Dedden, R.V.Nunez, K.Matoba, J.Takagi, C.Biertumpfel, N.Mizuno. Structural Insights Into Integrin Alpha 5 Beta 1 Opening By Fibronectin Ligand. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33962943
DOI: 10.1126/SCIADV.ABE9716
Page generated: Sun Oct 6 10:18:36 2024

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