3
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ATOM 22 N  GLN L 3 23.945 -2.849 106.974 1.00 15.00 N 
ATOM 23 CA GLN L 3 23.125 -2.052 106.036 1.00 15.00 C 
ATOM 24 C  GLN L 3 22.898 -0.648 106.616 1.00 15.00 C 
ATOM 25 O  GLN L 3 22.613 -0.491 107.825 1.00 15.00 O

In every amino acid there are two O atoms; which one is described by the (in this example) fourth entry? (I guess it's the one that's next to the next amino acid's N, but then where are the coordinates of the other one or should this be obvious?)

ATOM 26 CB   GLN L 3 21.754 -2.682 105.749 1.00 15.00 C 
ATOM 27 CG   GLN L 3 21.577 -3.299 104.379 1.00 15.00 C 
ATOM 28 CD   GLN L 3 20.956 -4.676 104.431 1.00 15.00 C 
ATOM 29 OE1  GLN L 3 20.940 -5.348 105.476 1.00 15.00 O 
ATOM 30 NE2  GLN L 3 20.496 -5.137 103.279 1.00 15.00 N 
ATOM 31 H    GLN L 3 24.339 -2.372 107.727 1.00 0.00  H 
ATOM 32 HE21 GLN L 3 20.637 -4.559 102.496 1.00 0.00  H 
ATOM 33 HE22 GLN L 3 20.049 -6.007 103.275 1.00 0.00  H 

What's this entry's nr.31 supposed to describe? I thought that an entry without remoteness indicator (and branch designator) might be bound to the previous atom, but in this case the N's adjacent H atoms are already dealt with with entries 32 and 33.

Also, this doesn't quite follow the convention(?)* of increasing the branch designator by one each time a new branch emerges—is this usual when H atoms' positions are given as well?

* like here:

ATOM 1661 CG  TRP A 214 24.705  7.905 6.526 1.00 50.03 C  
ATOM 1662 CD1 TRP A 214 23.435  7.531 6.857 1.00 49.65 C  
ATOM 1663 CD2 TRP A 214 25.087  8.914 7.475 1.00 51.52 C  
ATOM 1664 NE1 TRP A 214 22.999  8.246 7.947 1.00 51.68 N  
ATOM 1665 CE2 TRP A 214 23.993  9.098 8.350 1.00 52.47 C  
ATOM 1666 CE3 TRP A 214 26.251  9.675 7.670 1.00 52.68 C  
ATOM 1667 CZ2 TRP A 214 24.019 10.027 9.407 1.00 54.73 C  
ATOM 1668 CZ3 TRP A 214 26.279 10.600 8.724 1.00 53.86 C  
ATOM 1669 CH2 TRP A 214 25.167 10.761 9.581 1.00 54.84 C  
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4
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First, your PDB data seems to have some formatting issues, in that the columns are in the wrong places. I'm not sure if it's actually messed up, or if it simply got messed up when you posted it.

"In every amino acid there are two O atoms": True for a single amino acid; not true for an amino acid residue. I presume you're referring to the two oxygens on the carboxyl group. However, one of these is lost when the amino acid forms an amide linkage with the next amino acid.

"What's this entry's nr.31 supposed to describe? ": I opened the PDB in PyMol (after I corrected the format), and it seems to be the amide hydrogen

Regarding the branch designator -- I've never heard of such a thing in a PDB file, and I don't see any mention of it in the format description. Could you clarify?

ETA: I've tried to post the correctly formatted PDB data, but it seems to be messing up the formatting. I'll try to figure out how to do that. Here's an image of the residue enter image description here

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  • $\begingroup$ Regarding the branch designator: That's a term I found here haldane.bu.edu/needle-doc/new/atom-format.html; it's the number in the "atom name" field. Thanks for the extensive answer! (and yes, the formatting got pretty messed up when inserting it here) $\endgroup$ – Peter May 3 '15 at 21:32

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