Atomistry » Manganese » PDB 7mxs-7ohg » 7nwl
Atomistry »
  Manganese »
    PDB 7mxs-7ohg »
      7nwl »

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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Go back to Manganese Binding Sites List in 7nwl
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy